HEADER DNA BINDING PROTEIN/DNA 29-MAY-03 1PHJ TITLE CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- TITLE 2 BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GG(3DR) TITLE 3 GTTTTGGGG COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*GP*T)-3'; COMPND 3 CHAIN: G, H; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: 3' TERMINAL SINGLE STRAND DNA SEQUENCE OF COMPND 6 MACRONUCLEAR TELOMERES.; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-D(*GP*GP*(3DR)P*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'; COMPND 9 CHAIN: D; COMPND 10 ENGINEERED: YES; COMPND 11 MUTATION: YES; COMPND 12 OTHER_DETAILS: 3' TERMINAL SINGLE STRAND DNA SEQUENCE OF COMPND 13 MACRONUCLEAR TELOMERES, G TO 3DR SUBSTITUTION.; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: TELOMERE-BINDING PROTEIN ALPHA SUBUNIT; COMPND 16 CHAIN: A; COMPND 17 SYNONYM: TELOMERE-BINDING PROTEIN 56 KDA SUBUNIT, TEBP COMPND 18 ALPHA; COMPND 19 ENGINEERED: YES; COMPND 20 MOL_ID: 4; COMPND 21 MOLECULE: TELOMERE-BINDING PROTEIN BETA SUBUNIT; COMPND 22 CHAIN: B; COMPND 23 FRAGMENT: RESIDUES 9-224; COMPND 24 SYNONYM: TELOMERE-BINDING PROTEIN 41 KDA SUBUNIT, TEBP COMPND 25 BETA; COMPND 26 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: STERKIELLA NOVA; SOURCE 7 ORGANISM_TAXID: 200597; SOURCE 8 GENE: MAC-56A AND MAC-56K AND MAC-56S; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 12 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 13 EXPRESSION_SYSTEM_PLASMID: PKKT7; SOURCE 14 MOL_ID: 4; SOURCE 15 ORGANISM_SCIENTIFIC: STERKIELLA NOVA; SOURCE 16 ORGANISM_TAXID: 200597; SOURCE 17 GENE: MAC-41A AND MAC-41S; SOURCE 18 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 20 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 21 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 22 EXPRESSION_SYSTEM_PLASMID: PKKT7 KEYWDS SINGLE STRAND DNA BINDING PROTEIN, PROTEIN DNA INTERACTIONS, KEYWDS 2 SEQUENCE SPECIFICITY, NONCOGNATE, OLIGONUCLEOTIDE AND KEYWDS 3 OLIGOSACCHARIDE BINDING FOLD, OB FOLD, TELOMERES, KEYWDS 4 PROTEIN/DNA, DNA BINDING PROTEIN/DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.L.THEOBALD,S.C.SCHULTZ REVDAT 3 24-FEB-09 1PHJ 1 VERSN REVDAT 2 25-NOV-03 1PHJ 1 JRNL REVDAT 1 17-JUN-03 1PHJ 0 JRNL AUTH D.L.THEOBALD,S.C.SCHULTZ JRNL TITL NUCLEOTIDE SHUFFLING AND SSDNA RECOGNITION IN JRNL TITL 2 OXYTRICHA NOVA TELOMERE END-BINDING PROTEIN JRNL TITL 3 COMPLEXES JRNL REF EMBO J. V. 22 4314 2003 JRNL REFN ISSN 0261-4189 JRNL PMID 12912928 JRNL DOI 10.1093/EMBOJ/CDG415 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.31 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 228353.910 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.9 REMARK 3 NUMBER OF REFLECTIONS : 36489 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) : 0.246 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 3594 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.66 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5115 REMARK 3 BIN R VALUE (WORKING SET) : 0.2930 REMARK 3 BIN FREE R VALUE : 0.3430 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 526 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.015 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5359 REMARK 3 NUCLEIC ACID ATOMS : 748 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 303 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.26000 REMARK 3 B22 (A**2) : 4.26000 REMARK 3 B33 (A**2) : -8.52000 REMARK 3 B12 (A**2) : 1.71000 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) : 0.35 REMARK 3 ESD FROM SIGMAA (A) : 0.34 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) : 0.39 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.39 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.052 REMARK 3 BOND ANGLES (DEGREES) : 2.70 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.19 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) : 1.270 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.070 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.600 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.840 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.32 REMARK 3 BSOL : 23.53 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_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : WATER.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1PHJ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JUN-03. REMARK 100 THE RCSB ID CODE IS RCSB019327. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 83 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36489 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 27.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 141.16233 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 282.32467 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 211.74350 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 352.90583 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 70.58117 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 141.16233 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 282.32467 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 352.90583 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 211.74350 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 70.58117 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: PENTAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: G, D, H, A, B 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 DT G 13 REMARK 465 DT H 13 REMARK 465 GLN A 88 REMARK 465 LYS A 89 REMARK 465 GLY A 90 REMARK 465 ALA A 91 REMARK 465 GLY A 92 REMARK 465 GLY A 402 REMARK 465 ALA A 403 REMARK 465 SER A 404 REMARK 465 GLY A 405 REMARK 465 LEU A 493 REMARK 465 ILE A 494 REMARK 465 TYR A 495 REMARK 465 GLN B 9 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 OG SER A 323 O HOH A 629 2.11 REMARK 500 O LYS A 401 O HOH A 708 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 SER A 323 CA SER A 323 C -0.175 REMARK 500 LYS A 401 CB LYS A 401 CG 0.260 REMARK 500 LYS A 401 CD LYS A 401 CE 0.165 REMARK 500 LYS A 401 CA LYS A 401 C 0.166 REMARK 500 LYS A 406 N LYS A 406 CA 0.140 REMARK 500 LYS A 406 CA LYS A 406 C 0.172 REMARK 500 GLY A 407 CA GLY A 407 C 0.098 REMARK 500 LYS A 492 N LYS A 492 CA 0.129 REMARK 500 LYS A 492 CA LYS A 492 C 0.265 REMARK 500 GLN B 10 N GLN B 10 CA 0.542 REMARK 500 GLN B 10 CB GLN B 10 CG 0.192 REMARK 500 GLN B 10 CA GLN B 10 C 0.459 REMARK 500 GLN B 11 N GLN B 11 CA 0.166 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 G 9 C5' - C4' - C3' ANGL. DEV. = 7.9 DEGREES REMARK 500 DG G 10 C5' - C4' - C3' ANGL. DEV. = 7.4 DEGREES REMARK 500 LYS A 86 N - CA - C ANGL. DEV. = -22.5 DEGREES REMARK 500 GLN A 87 CB - CA - C ANGL. DEV. = 15.4 DEGREES REMARK 500 ASP A 93 C - N - CA ANGL. DEV. = 17.9 DEGREES REMARK 500 SER A 323 N - CA - CB ANGL. DEV. = 9.5 DEGREES REMARK 500 LEU A 400 CA - CB - CG ANGL. DEV. = -22.6 DEGREES REMARK 500 LYS A 401 CB - CA - C ANGL. DEV. = 17.4 DEGREES REMARK 500 LYS A 401 N - CA - C ANGL. DEV. = -24.3 DEGREES REMARK 500 LYS A 406 N - CA - C ANGL. DEV. = 26.3 DEGREES REMARK 500 GLY A 407 N - CA - C ANGL. DEV. = 16.3 DEGREES REMARK 500 ASP A 408 N - CA - C ANGL. DEV. = -19.6 DEGREES REMARK 500 GLN B 10 CB - CA - C ANGL. DEV. = -26.3 DEGREES REMARK 500 GLN B 10 N - CA - C ANGL. DEV. = 45.2 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 SER A 48 96.49 -69.64 REMARK 500 ALA A 49 36.83 -69.21 REMARK 500 ALA A 61 141.32 -176.55 REMARK 500 ASN A 68 -147.01 -159.34 REMARK 500 PRO A 81 -17.85 -46.41 REMARK 500 TYR A 84 -19.87 -147.77 REMARK 500 ASP A 93 -60.34 111.67 REMARK 500 TYR A 142 -83.43 -116.25 REMARK 500 SER A 176 168.49 73.02 REMARK 500 VAL A 205 -64.60 67.22 REMARK 500 SER A 275 99.51 73.85 REMARK 500 GLU A 320 -104.88 -77.28 REMARK 500 VAL A 321 -56.63 5.49 REMARK 500 ALA A 322 -17.87 -47.12 REMARK 500 SER A 359 -39.42 -135.96 REMARK 500 LYS A 406 106.23 161.09 REMARK 500 ASN A 483 49.27 39.43 REMARK 500 GLU B 25 55.52 31.64 REMARK 500 SER B 32 135.45 -35.13 REMARK 500 LYS B 36 39.95 -91.41 REMARK 500 TYR B 56 -36.67 -145.50 REMARK 500 HIS B 72 -7.67 -58.86 REMARK 500 ASN B 77 -12.90 70.25 REMARK 500 THR B 107 54.02 -95.11 REMARK 500 GLN B 126 65.59 -49.30 REMARK 500 GLU B 127 43.70 34.72 REMARK 500 LEU B 129 -161.13 -119.34 REMARK 500 ASN B 130 107.25 136.22 REMARK 500 ASP B 167 65.47 34.92 REMARK 500 ASP B 177 34.90 -152.15 REMARK 500 ALA B 178 38.76 -81.96 REMARK 500 GLU B 207 103.92 -50.01 REMARK 500 ASN B 209 -90.62 -98.75 REMARK 500 THR B 210 111.53 57.68 REMARK 500 LYS B 223 52.48 -155.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLN B 10 -13.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1OTC RELATED DB: PDB REMARK 900 SAME PROTEIN (ALPHA AND BETA SUBUNITS) COMPLEXED WITH REMARK 900 COGNATE SSDNA GGGGTTTTGGGG REMARK 900 RELATED ID: 1JB7 RELATED DB: PDB REMARK 900 SAME PROTEIN (ALPHA AND BETA SUBUNITS) COMPLEXED WITH REMARK 900 COGNATE SSDNA GGGGTTTTGGGG REMARK 900 RELATED ID: 1KIX RELATED DB: PDB REMARK 900 DIMER OF ALPHA SUBUNIT ALONE COMPLEXED WITH TTTTGGGG REMARK 900 RELATED ID: 1K8G RELATED DB: PDB REMARK 900 35 KDA N-TERMINAL FRAGMENT OF ALPHA SUBUNIT ALONE COMPLEXED REMARK 900 WITH TTGGGG REMARK 900 RELATED ID: 1PA6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- REMARK 900 BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGAGG REMARK 900 RELATED ID: 1PH1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- REMARK 900 BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA REMARK 900 GGGGTTTTGGGGT REMARK 900 RELATED ID: 1PH2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- REMARK 900 BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTG REMARK 900 RELATED ID: 1PH3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- REMARK 900 BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGGTG REMARK 900 RELATED ID: 1PH4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- REMARK 900 BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGGCG REMARK 900 RELATED ID: 1PH5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- REMARK 900 BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA REMARK 900 GGGGTTTTG(3DR)GG REMARK 900 RELATED ID: 1PH6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- REMARK 900 BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGTGG REMARK 900 RELATED ID: 1PH7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- REMARK 900 BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGIGG REMARK 900 RELATED ID: 1PH8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- REMARK 900 BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGCGG REMARK 900 RELATED ID: 1PH9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END- REMARK 900 BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGAGG DBREF 1PHJ A 35 495 UNP P29549 TEBA_OXYNO 35 495 DBREF 1PHJ B 9 224 UNP P16458 TEBB_OXYNO 9 224 DBREF 1PHJ G 1 13 PDB 1PHJ 1PHJ 1 13 DBREF 1PHJ D 1 12 PDB 1PHJ 1PHJ 1 12 DBREF 1PHJ H 1 13 PDB 1PHJ 1PHJ 1 13 SEQRES 1 G 13 DG DG DG DG DT DT DT DT DG DG DG DG DT SEQRES 1 D 12 DG DG 3DR DG DT DT DT DT DG DG DG DG SEQRES 1 H 13 DG DG DG DG DT DT DT DT DG DG DG DG DT SEQRES 1 A 461 LYS TYR GLU TYR VAL GLU LEU ALA LYS ALA SER LEU THR SEQRES 2 A 461 SER ALA GLN PRO GLN HIS PHE TYR ALA VAL VAL ILE ASP SEQRES 3 A 461 ALA THR PHE PRO TYR LYS THR ASN GLN GLU ARG TYR ILE SEQRES 4 A 461 CYS SER LEU LYS ILE VAL ASP PRO THR LEU TYR LEU LYS SEQRES 5 A 461 GLN GLN LYS GLY ALA GLY ASP ALA SER ASP TYR ALA THR SEQRES 6 A 461 LEU VAL LEU TYR ALA LYS ARG PHE GLU ASP LEU PRO ILE SEQRES 7 A 461 ILE HIS ARG ALA GLY ASP ILE ILE ARG VAL HIS ARG ALA SEQRES 8 A 461 THR LEU ARG LEU TYR ASN GLY GLN ARG GLN PHE ASN ALA SEQRES 9 A 461 ASN VAL PHE TYR SER SER SER TRP ALA LEU PHE SER THR SEQRES 10 A 461 ASP LYS ARG SER VAL THR GLN GLU ILE ASN ASN GLN ASP SEQRES 11 A 461 ALA VAL SER ASP THR THR PRO PHE SER PHE SER SER LYS SEQRES 12 A 461 HIS ALA THR ILE GLU LYS ASN GLU ILE SER ILE LEU GLN SEQRES 13 A 461 ASN LEU ARG LYS TRP ALA ASN GLN TYR PHE SER SER TYR SEQRES 14 A 461 SER VAL ILE SER SER ASP MET TYR THR ALA LEU ASN LYS SEQRES 15 A 461 ALA GLN ALA GLN LYS GLY ASP PHE ASP VAL VAL ALA LYS SEQRES 16 A 461 ILE LEU GLN VAL HIS GLU LEU ASP GLU TYR THR ASN GLU SEQRES 17 A 461 LEU LYS LEU LYS ASP ALA SER GLY GLN VAL PHE TYR THR SEQRES 18 A 461 LEU SER LEU LYS LEU LYS PHE PRO HIS VAL ARG THR GLY SEQRES 19 A 461 GLU VAL VAL ARG ILE ARG SER ALA THR TYR ASP GLU THR SEQRES 20 A 461 SER THR GLN LYS LYS VAL LEU ILE LEU SER HIS TYR SER SEQRES 21 A 461 ASN ILE ILE THR PHE ILE GLN SER SER LYS LEU ALA LYS SEQRES 22 A 461 GLU LEU ARG ALA LYS ILE GLN ASP ASP HIS SER VAL GLU SEQRES 23 A 461 VAL ALA SER LEU LYS LYS ASN VAL SER LEU ASN ALA VAL SEQRES 24 A 461 VAL LEU THR GLU VAL ASP LYS LYS HIS ALA ALA LEU PRO SEQRES 25 A 461 SER THR SER LEU GLN ASP LEU PHE HIS HIS ALA ASP SER SEQRES 26 A 461 ASP LYS GLU LEU GLN ALA GLN ASP THR PHE ARG THR GLN SEQRES 27 A 461 PHE TYR VAL THR LYS ILE GLU PRO SER ASP VAL LYS GLU SEQRES 28 A 461 TRP VAL LYS GLY TYR ASP ARG LYS THR LYS LYS SER SER SEQRES 29 A 461 SER LEU LYS GLY ALA SER GLY LYS GLY ASP ASN ILE PHE SEQRES 30 A 461 GLN VAL GLN PHE LEU VAL LYS ASP ALA SER THR GLN LEU SEQRES 31 A 461 ASN ASN ASN THR TYR ARG VAL LEU LEU TYR THR GLN ASP SEQRES 32 A 461 GLY LEU GLY ALA ASN PHE PHE ASN VAL LYS ALA ASP ASN SEQRES 33 A 461 LEU HIS LYS ASN ALA ASP ALA ARG LYS LYS LEU GLU ASP SEQRES 34 A 461 SER ALA GLU LEU LEU THR LYS PHE ASN SER TYR VAL ASP SEQRES 35 A 461 ALA VAL VAL GLU ARG ARG ASN GLY PHE TYR LEU ILE LYS SEQRES 36 A 461 ASP THR LYS LEU ILE TYR SEQRES 1 B 216 GLN GLN GLN SER ALA PHE LYS GLN LEU TYR THR GLU LEU SEQRES 2 B 216 PHE ASN ASN GLU GLY ASP PHE SER LYS VAL SER SER ASN SEQRES 3 B 216 LEU LYS LYS PRO LEU LYS CYS TYR VAL LYS GLU SER TYR SEQRES 4 B 216 PRO HIS PHE LEU VAL THR ASP GLY TYR PHE PHE VAL ALA SEQRES 5 B 216 PRO TYR PHE THR LYS GLU ALA VAL ASN GLU PHE HIS ALA SEQRES 6 B 216 LYS PHE PRO ASN VAL ASN ILE VAL ASP LEU THR ASP LYS SEQRES 7 B 216 VAL ILE VAL ILE ASN ASN TRP SER LEU GLU LEU ARG ARG SEQRES 8 B 216 VAL ASN SER ALA GLU VAL PHE THR SER TYR ALA ASN LEU SEQRES 9 B 216 GLU ALA ARG LEU ILE VAL HIS SER PHE LYS PRO ASN LEU SEQRES 10 B 216 GLN GLU ARG LEU ASN PRO THR ARG TYR PRO VAL ASN LEU SEQRES 11 B 216 PHE ARG ASP ASP GLU PHE LYS THR THR ILE GLN HIS PHE SEQRES 12 B 216 ARG HIS THR ALA LEU GLN ALA ALA ILE ASN LYS THR VAL SEQRES 13 B 216 LYS GLY ASP ASN LEU VAL ASP ILE SER LYS VAL ALA ASP SEQRES 14 B 216 ALA ALA GLY LYS LYS GLY LYS VAL ASP ALA GLY ILE VAL SEQRES 15 B 216 LYS ALA SER ALA SER LYS GLY ASP GLU PHE SER ASP PHE SEQRES 16 B 216 SER PHE LYS GLU GLY ASN THR ALA THR LEU LYS ILE ALA SEQRES 17 B 216 ASP ILE PHE VAL GLN GLU LYS GLY HET 3DR D 3 11 HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETSYN 3DR ABASIC DIDEOXYRIBOSE FORMUL 2 3DR C5 H11 O6 P FORMUL 6 HOH *303(H2 O) HELIX 1 1 ARG A 106 LEU A 110 5 5 HELIX 2 2 SER A 155 ASN A 162 1 8 HELIX 3 3 ASN A 184 TYR A 203 1 20 HELIX 4 4 SER A 207 TYR A 211 5 5 HELIX 5 5 ALA A 213 GLN A 220 5 8 HELIX 6 6 SER A 303 ILE A 313 1 11 HELIX 7 7 HIS A 317 ALA A 322 1 6 HELIX 8 8 SER A 323 LYS A 326 5 4 HELIX 9 9 LYS A 340 ALA A 343 5 4 HELIX 10 10 SER A 349 HIS A 356 1 8 HELIX 11 11 ASP A 360 ALA A 365 1 6 HELIX 12 12 ASP A 382 GLU A 385 5 4 HELIX 13 13 ASP A 419 GLN A 423 5 5 HELIX 14 14 ASN A 454 THR A 469 1 16 HELIX 15 15 SER B 12 ASN B 23 1 12 HELIX 16 16 SER B 32 LYS B 36 5 5 HELIX 17 17 THR B 64 PHE B 75 1 12 HELIX 18 18 ASN B 79 LEU B 83 5 5 HELIX 19 19 ASP B 141 VAL B 164 1 24 HELIX 20 20 ASP B 171 ASP B 177 1 7 HELIX 21 21 LYS B 184 ALA B 187 5 4 HELIX 22 22 ALA B 216 GLY B 224 1 9 SHEET 1 A 6 TYR A 65 LYS A 66 0 SHEET 2 A 6 TYR A 72 VAL A 79 -1 O ILE A 73 N TYR A 65 SHEET 3 A 6 GLN A 52 ALA A 61 -1 N VAL A 57 O VAL A 79 SHEET 4 A 6 ILE A 119 TYR A 130 -1 O ALA A 125 N GLN A 52 SHEET 5 A 6 SER A 145 PHE A 149 -1 O PHE A 149 N ILE A 119 SHEET 6 A 6 SER A 173 PHE A 174 -1 O SER A 173 N LEU A 148 SHEET 1 B 7 TYR A 65 LYS A 66 0 SHEET 2 B 7 TYR A 72 VAL A 79 -1 O ILE A 73 N TYR A 65 SHEET 3 B 7 ALA A 98 ALA A 104 -1 O LEU A 100 N LEU A 76 SHEET 4 B 7 GLN A 133 ASN A 139 1 O PHE A 136 N THR A 99 SHEET 5 B 7 ILE A 119 TYR A 130 -1 N TYR A 130 O GLN A 133 SHEET 6 B 7 SER A 145 PHE A 149 -1 O PHE A 149 N ILE A 119 SHEET 7 B 7 SER A 173 PHE A 174 -1 O SER A 173 N LEU A 148 SHEET 1 C 7 ARG A 115 ALA A 116 0 SHEET 2 C 7 VAL A 287 PHE A 299 1 O THR A 298 N ALA A 116 SHEET 3 C 7 VAL A 270 TYR A 278 -1 N ARG A 274 O ASN A 295 SHEET 4 C 7 PHE A 224 GLU A 235 -1 N VAL A 226 O ILE A 273 SHEET 5 C 7 THR A 240 LYS A 246 -1 O GLU A 242 N HIS A 234 SHEET 6 C 7 VAL A 252 LEU A 258 -1 O SER A 257 N ASN A 241 SHEET 7 C 7 VAL A 287 PHE A 299 1 O LEU A 288 N TYR A 254 SHEET 1 D 6 LYS A 396 SER A 398 0 SHEET 2 D 6 VAL A 387 ASP A 391 -1 N ASP A 391 O LYS A 396 SHEET 3 D 6 ASP A 408 LYS A 418 -1 O ASP A 408 N TYR A 390 SHEET 4 D 6 THR A 368 GLU A 379 -1 N GLU A 379 O GLN A 414 SHEET 5 D 6 SER A 473 ARG A 482 -1 O VAL A 475 N PHE A 373 SHEET 6 D 6 VAL A 333 VAL A 334 1 N VAL A 333 O TYR A 474 SHEET 1 E 5 LYS A 396 SER A 398 0 SHEET 2 E 5 VAL A 387 ASP A 391 -1 N ASP A 391 O LYS A 396 SHEET 3 E 5 ASP A 408 LYS A 418 -1 O ASP A 408 N TYR A 390 SHEET 4 E 5 ASN A 427 TYR A 434 -1 O TYR A 429 N VAL A 417 SHEET 5 E 5 ILE B 189 LYS B 191 -1 O VAL B 190 N THR A 428 SHEET 1 F 5 ILE B 189 LYS B 191 0 SHEET 2 F 5 ASN A 427 TYR A 434 -1 N THR A 428 O VAL B 190 SHEET 3 F 5 PHE A 485 LYS A 489 1 O ILE A 488 N LEU A 432 SHEET 4 F 5 SER A 473 ARG A 482 -1 N ARG A 482 O PHE A 485 SHEET 5 F 5 VAL A 333 VAL A 334 1 N VAL A 333 O TYR A 474 SHEET 1 G 2 GLU A 337 VAL A 338 0 SHEET 2 G 2 THR A 491 LYS A 492 -1 O LYS A 492 N GLU A 337 SHEET 1 H 7 PRO B 61 PHE B 63 0 SHEET 2 H 7 LEU B 112 ASN B 124 1 O LEU B 116 N TYR B 62 SHEET 3 H 7 VAL B 87 ARG B 99 -1 N SER B 94 O ILE B 117 SHEET 4 H 7 LEU B 39 GLU B 45 -1 N LEU B 39 O ILE B 90 SHEET 5 H 7 LEU B 51 THR B 53 -1 O THR B 53 N TYR B 42 SHEET 6 H 7 PHE B 57 VAL B 59 -1 O VAL B 59 N VAL B 52 SHEET 7 H 7 VAL B 136 ASN B 137 1 O VAL B 136 N PHE B 58 LINK O3' DG D 2 P 3DR D 3 1555 1555 1.61 LINK O3' 3DR D 3 P DG D 4 1555 1555 1.61 CISPEP 1 GLU A 379 PRO A 380 0 -0.46 CISPEP 2 TYR B 47 PRO B 48 0 6.33 CRYST1 93.481 93.481 423.487 90.00 90.00 120.00 P 61 2 2 24 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 0.010697 0.006176 0.000000 0.00000 SCALE2 0.000000 0.012352 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002361 0.00000