HEADER TRANSFERASE/DNA 30-APR-99 1CLQ TITLE CRYSTAL STRUCTURE OF A REPLICATION FORK DNA POLYMERASE EDITING COMPLEX TITLE 2 AT 2.7 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*CP*GP*GP*AP*AP*CP*TP*AP*CP*T)-3'); COMPND 3 CHAIN: E; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*AP*GP*TP*AP*GP*TP*TP*CP*CP*GP*CP*G)-3'); COMPND 7 CHAIN: D; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: PROTEIN (DNA POLYMERASE); COMPND 11 CHAIN: A; COMPND 12 FRAGMENT: RESIDUES 1-903; COMPND 13 SYNONYM: GP43; COMPND 14 EC: 2.7.7.7; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: PRIMER-TEMPLATE DNA; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 MOL_ID: 3; SOURCE 7 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE RB69; SOURCE 8 ORGANISM_TAXID: 12353; SOURCE 9 GENE: GENE 43; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 12 EXPRESSION_SYSTEM_CELL_LINE: BL21(DE3) KEYWDS DNA POLYMERASE, GP43, PROOFREADING, EDITING, REPLICATION, KEYWDS 2 TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.SHAMOO,T.A.STEITZ REVDAT 4 02-AUG-23 1CLQ 1 REMARK LINK REVDAT 3 24-FEB-09 1CLQ 1 VERSN REVDAT 2 01-APR-03 1CLQ 1 JRNL REVDAT 1 28-OCT-99 1CLQ 0 JRNL AUTH Y.SHAMOO,T.A.STEITZ JRNL TITL BUILDING A REPLISOME FROM INTERACTING PIECES: SLIDING CLAMP JRNL TITL 2 COMPLEXED TO A PEPTIDE FROM DNA POLYMERASE AND A POLYMERASE JRNL TITL 3 EDITING COMPLEX. JRNL REF CELL(CAMBRIDGE,MASS.) V. 99 155 1999 JRNL REFN ISSN 0092-8674 JRNL PMID 10535734 JRNL DOI 10.1016/S0092-8674(00)81647-5 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 50031 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.230 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.700 REMARK 3 FREE R VALUE TEST SET COUNT : 4877 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 7206 REMARK 3 BIN R VALUE (WORKING SET) : 0.3470 REMARK 3 BIN FREE R VALUE : 0.3990 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 874 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.014 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7381 REMARK 3 NUCLEIC ACID ATOMS : 467 REMARK 3 HETEROGEN ATOMS : 37 REMARK 3 SOLVENT ATOMS : 221 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 50.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.89000 REMARK 3 B22 (A**2) : -4.89000 REMARK 3 B33 (A**2) : 9.79000 REMARK 3 B12 (A**2) : 4.74000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.37 REMARK 3 ESD FROM SIGMAA (A) : 0.54 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.48 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.69 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.180 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.990 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.650 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.690 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 6.830 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.31 REMARK 3 BSOL : 46.43 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : WATER.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1CLQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB. REMARK 100 THE DEPOSITION ID IS D_1000000982. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-OCT-98 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9188 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : SILICON 111 BENDING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51455 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 2.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08000 REMARK 200 FOR THE DATA SET : 18.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 1WAJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% (W/V) PEG 350MME, 150 MM CACL2, REMARK 280 100 MM SODIUM CACODYLATE, PH 6.5, 12 DEGREES C, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 285K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 104.87000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 60.54672 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 38.08333 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 104.87000 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 60.54672 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 38.08333 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 104.87000 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 60.54672 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 38.08333 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 121.09345 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 76.16667 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 121.09345 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 76.16667 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 121.09345 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 76.16667 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, D, A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O5' DG E 2 N ASN A 255 2.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DG E 2 O5' - C5' - C4' ANGL. DEV. = -7.7 DEGREES REMARK 500 DG E 2 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DA E 7 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT E 12 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 DA D 12 O5' - C5' - C4' ANGL. DEV. = -5.3 DEGREES REMARK 500 DA D 12 O4' - C1' - C2' ANGL. DEV. = 7.2 DEGREES REMARK 500 DA D 12 N9 - C1' - C2' ANGL. DEV. = 13.6 DEGREES REMARK 500 DA D 12 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 DA D 12 C8 - N9 - C1' ANGL. DEV. = 14.4 DEGREES REMARK 500 DA D 12 C4 - N9 - C1' ANGL. DEV. = -14.3 DEGREES REMARK 500 DA D 9 O4' - C1' - C2' ANGL. DEV. = 3.3 DEGREES REMARK 500 DG D 8 O4' - C1' - C2' ANGL. DEV. = 3.8 DEGREES REMARK 500 DC D 5 O4' - C1' - C2' ANGL. DEV. = 3.3 DEGREES REMARK 500 DC D 4 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 LEU A 412 CA - CB - CG ANGL. DEV. = 19.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLU A 43 15.39 -64.06 REMARK 500 THR A 47 -107.12 -128.66 REMARK 500 TYR A 99 156.46 176.20 REMARK 500 ASP A 121 -144.09 -76.02 REMARK 500 ILE A 136 115.27 -172.60 REMARK 500 LEU A 152 -4.60 -144.23 REMARK 500 ILE A 166 -71.46 -59.46 REMARK 500 ALA A 167 -39.72 -15.28 REMARK 500 GLU A 172 26.19 -61.41 REMARK 500 GLN A 173 -12.01 -151.71 REMARK 500 PRO A 179 146.30 -34.46 REMARK 500 GLU A 181 20.11 -61.34 REMARK 500 GLU A 196 -74.53 -59.47 REMARK 500 LYS A 208 63.68 -153.03 REMARK 500 ASN A 217 29.96 82.41 REMARK 500 PHE A 221 -69.08 -141.62 REMARK 500 LYS A 240 0.02 -69.55 REMARK 500 MET A 256 -80.85 44.89 REMARK 500 LYS A 302 93.50 -61.32 REMARK 500 LEU A 303 122.65 -34.07 REMARK 500 TYR A 305 134.61 -174.46 REMARK 500 LYS A 352 67.22 64.26 REMARK 500 ASN A 402 -178.30 179.12 REMARK 500 SER A 414 52.09 28.54 REMARK 500 ASN A 424 46.95 78.04 REMARK 500 LEU A 508 98.77 -61.08 REMARK 500 SER A 509 -170.87 179.39 REMARK 500 ASP A 511 -157.18 -140.92 REMARK 500 LYS A 536 -73.28 -61.24 REMARK 500 ASP A 621 -154.90 -76.16 REMARK 500 ASP A 623 11.41 -143.55 REMARK 500 ARG A 642 -89.20 -57.97 REMARK 500 ASN A 645 -2.75 -59.28 REMARK 500 ASN A 675 74.95 50.96 REMARK 500 LYS A 739 -39.44 -37.33 REMARK 500 ALA A 780 -173.62 -61.59 REMARK 500 SER A 783 171.29 175.31 REMARK 500 ASN A 787 56.07 153.81 REMARK 500 GLU A 828 -165.28 -67.90 REMARK 500 ILE A 854 131.29 -38.71 REMARK 500 LYS A 888 43.02 71.85 REMARK 500 LEU A 897 -37.12 -25.76 REMARK 500 ASP A 899 39.35 -74.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DT E 12 0.20 SIDE CHAIN REMARK 500 TYR A 567 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA E1024 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DA E 10 O3' REMARK 620 2 DC E 11 O5' 56.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA D1003 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG D 1 OP1 REMARK 620 2 DC D 2 O3' 54.0 REMARK 620 3 ASP A 114 OD2 90.4 143.4 REMARK 620 4 ASP A 114 OD1 119.3 150.8 50.3 REMARK 620 5 HOH A1185 O 145.1 91.9 124.4 86.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1002 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG D 1 OP1 REMARK 620 2 GLU A 116 OE1 84.2 REMARK 620 3 GLU A 116 OE2 107.3 44.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA D1009 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT D 7 O5' REMARK 620 2 DT D 7 OP2 49.6 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1004 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 219 OE1 REMARK 620 2 ASP A 275 OD1 84.8 REMARK 620 3 ASP A 275 OD2 73.6 52.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1001 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 505 O REMARK 620 2 ASN A 507 OD1 83.3 REMARK 620 3 LYS A 531 O 146.7 70.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1025 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 621 OD2 REMARK 620 2 ASP A 623 OD1 71.0 REMARK 620 3 SER A 624 OG 63.8 59.9 REMARK 620 4 HOH A1071 O 110.8 104.6 164.2 REMARK 620 5 HOH A1150 O 145.6 78.4 113.2 62.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1006 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 676 O REMARK 620 2 ASN A 676 N 55.5 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA D 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1006 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA D 1009 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA E 1024 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1025 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP A 999 DBREF 1CLQ A 1 903 UNP Q38087 DPOL_BPR69 1 903 DBREF 1CLQ E 2 12 PDB 1CLQ 1CLQ 2 12 DBREF 1CLQ D 12 1 PDB 1CLQ 1CLQ 12 1 SEQRES 1 E 11 DG DC DG DG DA DA DC DT DA DC DT SEQRES 1 D 12 DA DG DT DA DG DT DT DC DC DG DC DG SEQRES 1 A 903 MET LYS GLU PHE TYR LEU THR VAL GLU GLN ILE GLY ASP SEQRES 2 A 903 SER ILE PHE GLU ARG TYR ILE ASP SER ASN GLY ARG GLU SEQRES 3 A 903 ARG THR ARG GLU VAL GLU TYR LYS PRO SER LEU PHE ALA SEQRES 4 A 903 HIS CYS PRO GLU SER GLN ALA THR LYS TYR PHE ASP ILE SEQRES 5 A 903 TYR GLY LYS PRO CYS THR ARG LYS LEU PHE ALA ASN MET SEQRES 6 A 903 ARG ASP ALA SER GLN TRP ILE LYS ARG MET GLU ASP ILE SEQRES 7 A 903 GLY LEU GLU ALA LEU GLY MET ASP ASP PHE LYS LEU ALA SEQRES 8 A 903 TYR LEU SER ASP THR TYR ASN TYR GLU ILE LYS TYR ASP SEQRES 9 A 903 HIS THR LYS ILE ARG VAL ALA ASN PHE ASP ILE GLU VAL SEQRES 10 A 903 THR SER PRO ASP GLY PHE PRO GLU PRO SER GLN ALA LYS SEQRES 11 A 903 HIS PRO ILE ASP ALA ILE THR HIS TYR ASP SER ILE ASP SEQRES 12 A 903 ASP ARG PHE TYR VAL PHE ASP LEU LEU ASN SER PRO TYR SEQRES 13 A 903 GLY ASN VAL GLU GLU TRP SER ILE GLU ILE ALA ALA LYS SEQRES 14 A 903 LEU GLN GLU GLN GLY GLY ASP GLU VAL PRO SER GLU ILE SEQRES 15 A 903 ILE ASP LYS ILE ILE TYR MET PRO PHE ASP ASN GLU LYS SEQRES 16 A 903 GLU LEU LEU MET GLU TYR LEU ASN PHE TRP GLN GLN LYS SEQRES 17 A 903 THR PRO VAL ILE LEU THR GLY TRP ASN VAL GLU SER PHE SEQRES 18 A 903 ASP ILE PRO TYR VAL TYR ASN ARG ILE LYS ASN ILE PHE SEQRES 19 A 903 GLY GLU SER THR ALA LYS ARG LEU SER PRO HIS ARG LYS SEQRES 20 A 903 THR ARG VAL LYS VAL ILE GLU ASN MET TYR GLY SER ARG SEQRES 21 A 903 GLU ILE ILE THR LEU PHE GLY ILE SER VAL LEU ASP TYR SEQRES 22 A 903 ILE ASP LEU TYR LYS LYS PHE SER PHE THR ASN GLN PRO SEQRES 23 A 903 SER TYR SER LEU ASP TYR ILE SER GLU PHE GLU LEU ASN SEQRES 24 A 903 VAL GLY LYS LEU LYS TYR ASP GLY PRO ILE SER LYS LEU SEQRES 25 A 903 ARG GLU SER ASN HIS GLN ARG TYR ILE SER TYR ASN ILE SEQRES 26 A 903 ILE ASP VAL TYR ARG VAL LEU GLN ILE ASP ALA LYS ARG SEQRES 27 A 903 GLN PHE ILE ASN LEU SER LEU ASP MET GLY TYR TYR ALA SEQRES 28 A 903 LYS ILE GLN ILE GLN SER VAL PHE SER PRO ILE LYS THR SEQRES 29 A 903 TRP ASP ALA ILE ILE PHE ASN SER LEU LYS GLU GLN ASN SEQRES 30 A 903 LYS VAL ILE PRO GLN GLY ARG SER HIS PRO VAL GLN PRO SEQRES 31 A 903 TYR PRO GLY ALA PHE VAL LYS GLU PRO ILE PRO ASN ARG SEQRES 32 A 903 TYR LYS TYR VAL MET SER PHE ASP LEU THR SER LEU TYR SEQRES 33 A 903 PRO SER ILE ILE ARG GLN VAL ASN ILE SER PRO GLU THR SEQRES 34 A 903 ILE ALA GLY THR PHE LYS VAL ALA PRO LEU HIS ASP TYR SEQRES 35 A 903 ILE ASN ALA VAL ALA GLU ARG PRO SER ASP VAL TYR SER SEQRES 36 A 903 CYS SER PRO ASN GLY MET MET TYR TYR LYS ASP ARG ASP SEQRES 37 A 903 GLY VAL VAL PRO THR GLU ILE THR LYS VAL PHE ASN GLN SEQRES 38 A 903 ARG LYS GLU HIS LYS GLY TYR MET LEU ALA ALA GLN ARG SEQRES 39 A 903 ASN GLY GLU ILE ILE LYS GLU ALA LEU HIS ASN PRO ASN SEQRES 40 A 903 LEU SER VAL ASP GLU PRO LEU ASP VAL ASP TYR ARG PHE SEQRES 41 A 903 ASP PHE SER ASP GLU ILE LYS GLU LYS ILE LYS LYS LEU SEQRES 42 A 903 SER ALA LYS SER LEU ASN GLU MET LEU PHE ARG ALA GLN SEQRES 43 A 903 ARG THR GLU VAL ALA GLY MET THR ALA GLN ILE ASN ARG SEQRES 44 A 903 LYS LEU LEU ILE ASN SER LEU TYR GLY ALA LEU GLY ASN SEQRES 45 A 903 VAL TRP PHE ARG TYR TYR ASP LEU ARG ASN ALA THR ALA SEQRES 46 A 903 ILE THR THR PHE GLY GLN MET ALA LEU GLN TRP ILE GLU SEQRES 47 A 903 ARG LYS VAL ASN GLU TYR LEU ASN GLU VAL CYS GLY THR SEQRES 48 A 903 GLU GLY GLU ALA PHE VAL LEU TYR GLY ASP THR ASP SER SEQRES 49 A 903 ILE TYR VAL SER ALA ASP LYS ILE ILE ASP LYS VAL GLY SEQRES 50 A 903 GLU SER LYS PHE ARG ASP THR ASN HIS TRP VAL ASP PHE SEQRES 51 A 903 LEU ASP LYS PHE ALA ARG GLU ARG MET GLU PRO ALA ILE SEQRES 52 A 903 ASP ARG GLY PHE ARG GLU MET CYS GLU TYR MET ASN ASN SEQRES 53 A 903 LYS GLN HIS LEU MET PHE MET ASP ARG GLU ALA ILE ALA SEQRES 54 A 903 GLY PRO PRO LEU GLY SER LYS GLY ILE GLY GLY PHE TRP SEQRES 55 A 903 THR GLY LYS LYS ARG TYR ALA LEU ASN VAL TRP ASP MET SEQRES 56 A 903 GLU GLY THR ARG TYR ALA GLU PRO LYS LEU LYS ILE MET SEQRES 57 A 903 GLY LEU GLU THR GLN LYS SER SER THR PRO LYS ALA VAL SEQRES 58 A 903 GLN LYS ALA LEU LYS GLU CYS ILE ARG ARG MET LEU GLN SEQRES 59 A 903 GLU GLY GLU GLU SER LEU GLN GLU TYR PHE LYS GLU PHE SEQRES 60 A 903 GLU LYS GLU PHE ARG GLN LEU ASN TYR ILE SER ILE ALA SEQRES 61 A 903 SER VAL SER SER ALA ASN ASN ILE ALA LYS TYR ASP VAL SEQRES 62 A 903 GLY GLY PHE PRO GLY PRO LYS CYS PRO PHE HIS ILE ARG SEQRES 63 A 903 GLY ILE LEU THR TYR ASN ARG ALA ILE LYS GLY ASN ILE SEQRES 64 A 903 ASP ALA PRO GLN VAL VAL GLU GLY GLU LYS VAL TYR VAL SEQRES 65 A 903 LEU PRO LEU ARG GLU GLY ASN PRO PHE GLY ASP LYS CYS SEQRES 66 A 903 ILE ALA TRP PRO SER GLY THR GLU ILE THR ASP LEU ILE SEQRES 67 A 903 LYS ASP ASP VAL LEU HIS TRP MET ASP TYR THR VAL LEU SEQRES 68 A 903 LEU GLU LYS THR PHE ILE LYS PRO LEU GLU GLY PHE THR SEQRES 69 A 903 SER ALA ALA LYS LEU ASP TYR GLU LYS LYS ALA SER LEU SEQRES 70 A 903 PHE ASP MET PHE ASP PHE HET CA E1024 1 HET CA D1003 1 HET CA D1009 1 HET CA A1001 1 HET CA A1002 1 HET CA A1004 1 HET CA A1005 1 HET CA A1006 1 HET CA A1025 1 HET GDP A 999 28 HETNAM CA CALCIUM ION HETNAM GDP GUANOSINE-5'-DIPHOSPHATE FORMUL 4 CA 9(CA 2+) FORMUL 13 GDP C10 H15 N5 O11 P2 FORMUL 14 HOH *221(H2 O) HELIX 1 1 MET A 65 ILE A 78 1 14 HELIX 2 2 PHE A 88 THR A 96 1 9 HELIX 3 3 HIS A 105 LYS A 107 5 3 HELIX 4 4 ILE A 164 ALA A 168 1 5 HELIX 5 5 GLN A 171 GLN A 173 5 3 HELIX 6 6 SER A 180 LYS A 185 1 6 HELIX 7 7 GLU A 194 GLN A 207 1 14 HELIX 8 8 ASP A 222 PHE A 234 1 13 HELIX 9 9 LYS A 240 LEU A 242 5 3 HELIX 10 10 TYR A 273 PHE A 280 1 8 HELIX 11 11 LEU A 290 LEU A 298 1 9 HELIX 12 12 ILE A 309 SER A 315 5 7 HELIX 13 13 HIS A 317 ARG A 338 1 22 HELIX 14 14 PHE A 340 ALA A 351 1 12 HELIX 15 15 ILE A 355 PHE A 359 5 5 HELIX 16 16 PRO A 361 GLN A 376 1 16 HELIX 17 17 LEU A 415 GLN A 422 1 8 HELIX 18 18 PRO A 427 THR A 429 5 3 HELIX 19 19 LEU A 439 ILE A 443 1 5 HELIX 20 20 VAL A 470 ASN A 505 1 36 HELIX 21 21 ASP A 524 LYS A 532 1 9 HELIX 22 22 ALA A 535 LEU A 570 1 36 HELIX 23 23 LEU A 580 VAL A 608 1 29 HELIX 24 24 ASP A 630 VAL A 636 1 7 HELIX 25 25 THR A 644 GLU A 657 1 14 HELIX 26 26 MET A 659 TYR A 673 1 15 HELIX 27 27 LYS A 739 GLN A 754 1 16 HELIX 28 28 GLU A 757 ARG A 772 1 16 HELIX 29 29 TYR A 776 ILE A 779 1 4 HELIX 30 30 ILE A 788 TYR A 791 1 4 HELIX 31 31 PHE A 803 ALA A 814 1 12 HELIX 32 32 LYS A 859 TRP A 865 1 7 HELIX 33 33 TYR A 868 THR A 875 1 8 HELIX 34 34 ILE A 877 ALA A 887 1 11 SHEET 1 A 3 GLU A 26 VAL A 31 0 SHEET 2 A 3 SER A 14 ILE A 20 -1 N TYR A 19 O ARG A 27 SHEET 3 A 3 PHE A 4 ILE A 11 -1 N ILE A 11 O SER A 14 SHEET 1 B 2 SER A 36 HIS A 40 0 SHEET 2 B 2 CYS A 57 LEU A 61 -1 N LYS A 60 O LEU A 37 SHEET 1 C 5 ILE A 212 THR A 214 0 SHEET 2 C 5 VAL A 110 GLU A 116 1 N ALA A 111 O ILE A 212 SHEET 3 C 5 ALA A 135 ASP A 140 -1 N TYR A 139 O ASN A 112 SHEET 4 C 5 ARG A 145 ASP A 150 -1 N TYR A 147 O HIS A 138 SHEET 5 C 5 ILE A 186 PRO A 190 1 N ILE A 187 O PHE A 146 SHEET 1 D 2 THR A 248 ASN A 255 0 SHEET 2 D 2 GLY A 258 LEU A 265 -1 N THR A 264 O ARG A 249 SHEET 1 E 6 LYS A 724 MET A 728 0 SHEET 2 E 6 TYR A 708 MET A 715 -1 N VAL A 712 O LYS A 724 SHEET 3 E 6 MET A 683 ALA A 689 -1 N ILE A 688 O TRP A 713 SHEET 4 E 6 VAL A 407 LEU A 412 -1 N ASP A 411 O ASP A 684 SHEET 5 E 6 SER A 624 SER A 628 -1 N VAL A 627 O MET A 408 SHEET 6 E 6 VAL A 617 GLY A 620 -1 N TYR A 619 O TYR A 626 SHEET 1 F 3 SER A 781 SER A 784 0 SHEET 2 F 3 LYS A 829 PRO A 834 -1 N VAL A 832 O SER A 781 SHEET 3 F 3 CYS A 845 PRO A 849 -1 N TRP A 848 O TYR A 831 SHEET 1 G 2 ILE A 430 THR A 433 0 SHEET 2 G 2 MET A 461 TYR A 463 -1 N MET A 462 O ALA A 431 SHEET 1 H 2 GLY A 700 GLY A 704 0 SHEET 2 H 2 ARG A 707 LEU A 710 -1 N ALA A 709 O PHE A 701 LINK O3' DA E 10 CA CA E1024 1555 1555 2.25 LINK O5' DC E 11 CA CA E1024 1555 1555 2.96 LINK OP1 DG D 1 CA CA D1003 1555 1555 2.66 LINK OP1 DG D 1 CA CA A1002 1555 1555 2.32 LINK O3' DC D 2 CA CA D1003 1555 1555 2.90 LINK O5' DT D 7 CA CA D1009 1555 1555 2.90 LINK OP2 DT D 7 CA CA D1009 1555 1555 3.02 LINK CA CA D1003 OD2 ASP A 114 1555 1555 2.83 LINK CA CA D1003 OD1 ASP A 114 1555 1555 2.05 LINK CA CA D1003 O HOH A1185 1555 1555 2.70 LINK OE1 GLU A 116 CA CA A1002 1555 1555 3.07 LINK OE2 GLU A 116 CA CA A1002 1555 1555 2.66 LINK OE1 GLU A 219 CA CA A1004 1555 1555 2.34 LINK OD1 ASP A 275 CA CA A1004 1555 1555 2.57 LINK OD2 ASP A 275 CA CA A1004 1555 1555 2.35 LINK O ASN A 505 CA CA A1001 1555 1555 2.29 LINK OD1 ASN A 507 CA CA A1001 1555 1555 2.43 LINK O LYS A 531 CA CA A1001 1555 1555 2.21 LINK OD2 ASP A 621 CA CA A1025 1555 1555 2.98 LINK OD1 ASP A 623 CA CA A1025 1555 1555 2.83 LINK OG SER A 624 CA CA A1025 1555 1555 2.87 LINK O ASN A 676 CA CA A1006 1555 1555 2.46 LINK N ASN A 676 CA CA A1006 1555 1555 3.33 LINK OE2 GLU A 716 CA CA A1005 1555 1555 3.00 LINK CA CA A1025 O HOH A1071 1555 1555 3.03 LINK CA CA A1025 O HOH A1150 1555 1555 3.07 SITE 1 AC1 3 ASN A 505 ASN A 507 LYS A 531 SITE 1 AC2 2 GLU A 116 DG D 1 SITE 1 AC3 4 ASP A 114 HOH A1185 DG D 1 DC D 2 SITE 1 AC4 2 GLU A 219 ASP A 275 SITE 1 AC5 1 GLU A 716 SITE 1 AC6 2 CYS A 671 ASN A 676 SITE 1 AC7 1 DT D 7 SITE 1 AC8 2 DA E 10 DC E 11 SITE 1 AC9 5 ASP A 621 ASP A 623 SER A 624 HOH A1071 SITE 2 AC9 5 HOH A1150 SITE 1 BC1 12 TYR A 33 SER A 36 PHE A 38 LYS A 48 SITE 2 BC1 12 TYR A 49 GLY A 84 MET A 85 ALA A 91 SITE 3 BC1 12 ASP A 95 LYS A 378 VAL A 379 ILE A 380 CRYST1 209.740 209.740 114.250 90.00 90.00 120.00 H 3 9 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.004768 0.002753 0.000000 0.00000 SCALE2 0.000000 0.005505 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008753 0.00000