HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 05-DEC-07 3BK5 TITLE CRYSTAL STRUCTURE OF PUTATIVE OUTER MEMBRANE LIPOPROTEIN-SORTING TITLE 2 PROTEIN DOMAIN FROM VIBRIO PARAHAEMOLYTICUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE OUTER MEMBRANE LIPOPROTEIN-SORTING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 28-261; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO PARAHAEMOLYTICUS RIMD 2210633; SOURCE 3 ORGANISM_TAXID: 223926; SOURCE 4 STRAIN: RIMD 2210633 / SEROTYPE O3:K6; SOURCE 5 GENE: VP1287; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PDM68 KEYWDS PUTATIVE OUTER MEMBRANE PROTEIN DOMAIN, PSI-2, PROTEIN STRUCTURE KEYWDS 2 INITIATIVE, STRUCTURAL GENOMICS, MIDWEST CENTER FOR STRUCTURAL KEYWDS 3 GENOMICS (MCSG), UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR R.WU,J.ABDULLAH,A.JOACHIMIAK,MIDWEST CENTER FOR STRUCTURAL GENOMICS AUTHOR 2 (MCSG) REVDAT 3 13-JUL-11 3BK5 1 VERSN REVDAT 2 24-FEB-09 3BK5 1 VERSN REVDAT 1 05-FEB-08 3BK5 0 JRNL AUTH R.WU,J.ABDULLAH,A.JOACHIMIAK JRNL TITL THE CRYSTAL STRUCTURE OF PUTATIVE OUTER MEMBRANE JRNL TITL 2 LIPOPROTEIN-SORTING PROTEIN DOMAIN FROM VIBRIO JRNL TITL 3 PARAHAEMOLYTICUS. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 17275 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 + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 937 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1128 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.26 REMARK 3 BIN R VALUE (WORKING SET) : 0.2170 REMARK 3 BIN FREE R VALUE SET COUNT : 76 REMARK 3 BIN FREE R VALUE : 0.2610 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1920 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 203 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 28.45 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.77 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.63000 REMARK 3 B22 (A**2) : -0.72000 REMARK 3 B33 (A**2) : 1.35000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.181 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.163 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.117 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.004 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1979 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2661 ; 1.641 ; 1.947 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 237 ; 9.325 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 104 ;34.487 ;24.327 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 372 ;15.228 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;22.270 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 279 ; 0.120 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1506 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 769 ; 0.213 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1302 ; 0.306 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 175 ; 0.168 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.028 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 33 ; 0.254 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 9 ; 0.189 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1219 ; 1.002 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1887 ; 1.546 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 876 ; 2.501 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 774 ; 3.812 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 5 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A -1 A 50 REMARK 3 RESIDUE RANGE : A 51 A 100 REMARK 3 RESIDUE RANGE : A 101 A 150 REMARK 3 RESIDUE RANGE : A 151 A 200 REMARK 3 RESIDUE RANGE : A 201 A 234 REMARK 3 ORIGIN FOR THE GROUP (A): 12.3809 18.4107 9.9460 REMARK 3 T TENSOR REMARK 3 T11: -0.0660 T22: -0.0817 REMARK 3 T33: -0.1090 T12: 0.0214 REMARK 3 T13: 0.0207 T23: 0.0107 REMARK 3 L TENSOR REMARK 3 L11: 2.7984 L22: 1.6796 REMARK 3 L33: 0.5194 L12: 0.3608 REMARK 3 L13: -0.0915 L23: -0.1237 REMARK 3 S TENSOR REMARK 3 S11: -0.0438 S12: 0.0372 S13: 0.0547 REMARK 3 S21: -0.0473 S22: 0.0365 S23: 0.0776 REMARK 3 S31: -0.0033 S32: 0.0060 S33: 0.0073 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3BK5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-DEC-07. REMARK 100 THE RCSB ID CODE IS RCSB045619. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUN-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97980 REMARK 200 MONOCHROMATOR : SI(111) CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17574 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.16100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.49300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M NA ACETATE, 20% PEG 8000, 0.2M REMARK 280 MGCL2, PH 4.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 24.07850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 64.43700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.07850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 64.43700 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 373 LIES ON A SPECIAL POSITION. 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 SER A -2 REMARK 465 GLY A 33 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 ALA A 31 C GLN A 32 N 0.178 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 ALA A 31 O - C - N ANGL. DEV. = -12.1 DEGREES REMARK 500 ARG A 93 NE - CZ - NH2 ANGL. DEV. = -3.3 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 ALA A 31 -155.91 -149.77 REMARK 500 MSE A 104 60.24 34.14 REMARK 500 ASP A 190 10.63 57.65 REMARK 500 LYS A 191 -54.70 -131.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 THR A 205 GLY A 206 -47.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 THR A 205 21.4 L L OUTSIDE RANGE 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 MG A 235 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 125 NE2 REMARK 620 2 ASP A 128 OD1 105.7 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 MG A 235 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: APC87289.2 RELATED DB: TARGETDB DBREF 3BK5 A 1 234 UNP Q87Q63 Q87Q63_VIBPA 28 261 SEQADV 3BK5 SER A -2 UNP Q87Q63 EXPRESSION TAG SEQADV 3BK5 ASN A -1 UNP Q87Q63 EXPRESSION TAG SEQADV 3BK5 ALA A 0 UNP Q87Q63 EXPRESSION TAG SEQRES 1 A 237 SER ASN ALA GLU LYS GLY LEU GLU ILE ALA GLN GLU ARG SEQRES 2 A 237 LYS ALA ARG ASP GLU GLY TRP GLY ASP SER ILE ALA THR SEQRES 3 A 237 MSE GLU MSE ILE LEU LYS ASN ALA GLN GLY GLU SER SER SEQRES 4 A 237 THR ARG LEU MSE ARG LEU LYS SER LEU GLU VAL GLU GLY SEQRES 5 A 237 ASP GLY ASP LYS GLY LEU THR ILE PHE ASP GLN PRO ARG SEQRES 6 A 237 ASP VAL THR GLY THR ALA PHE LEU ASN HIS SER HIS THR SEQRES 7 A 237 ILE GLY ALA ASP ASP GLN TRP LEU TYR LEU PRO ALA LEU SEQRES 8 A 237 LYS ARG VAL LYS ARG ILE SER SER ARG ASN LYS SER GLY SEQRES 9 A 237 PRO PHE MSE GLY SER GLU PHE ALA TYR GLU ASP LEU SER SEQRES 10 A 237 SER PHE GLU ILE GLU LYS TYR ARG PHE ASN HIS LEU LYS SEQRES 11 A 237 ASP GLU LYS PHE ASN GLY GLN ASP VAL PHE VAL LEU GLU SEQRES 12 A 237 GLN ILE PRO THR ASP LYS ASN SER GLY TYR THR LYS GLN SEQRES 13 A 237 VAL VAL TRP LEU ASP LYS ALA HIS TYR ARG PRO LEU LYS SEQRES 14 A 237 VAL GLU PHE TYR ASP ARG LYS GLY ALA LEU LEU LYS THR SEQRES 15 A 237 LEU THR PHE ALA ASN TYR LYS GLN TYR LEU ASP LYS TYR SEQRES 16 A 237 TRP ARG ALA HIS THR MSE ALA MSE THR ASN HIS GLN THR SEQRES 17 A 237 GLY LYS SER THR GLU LEU ASN THR SER ASP LEU ARG PHE SEQRES 18 A 237 GLN THR GLY LEU GLU GLU ASN ASP PHE ASN LYS ASN VAL SEQRES 19 A 237 LEU LYS ARG MODRES 3BK5 MSE A 24 MET SELENOMETHIONINE MODRES 3BK5 MSE A 26 MET SELENOMETHIONINE MODRES 3BK5 MSE A 40 MET SELENOMETHIONINE MODRES 3BK5 MSE A 104 MET SELENOMETHIONINE MODRES 3BK5 MSE A 198 MET SELENOMETHIONINE MODRES 3BK5 MSE A 200 MET SELENOMETHIONINE HET MSE A 24 8 HET MSE A 26 8 HET MSE A 40 8 HET MSE A 104 16 HET MSE A 198 8 HET MSE A 200 8 HET MG A 235 1 HETNAM MSE SELENOMETHIONINE HETNAM MG MAGNESIUM ION FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 2 MG MG 2+ FORMUL 3 HOH *203(H2 O) HELIX 1 1 ASN A -1 ARG A 13 1 15 HELIX 2 2 SER A 95 LYS A 99 5 5 HELIX 3 3 ALA A 109 SER A 114 5 6 HELIX 4 4 GLU A 117 GLU A 119 5 3 HELIX 5 5 GLU A 223 LEU A 232 5 10 SHEET 1 A13 ARG A 90 ARG A 93 0 SHEET 2 A13 ASP A 80 LEU A 85 -1 N LEU A 83 O LYS A 92 SHEET 3 A13 ALA A 68 HIS A 72 -1 N ALA A 68 O TYR A 84 SHEET 4 A13 LYS A 53 GLN A 60 -1 N THR A 56 O PHE A 69 SHEET 5 A13 SER A 36 LEU A 45 -1 N LEU A 39 O ASP A 59 SHEET 6 A13 ASP A 19 LYS A 29 -1 N LEU A 28 O SER A 36 SHEET 7 A13 SER A 208 PHE A 218 -1 O SER A 208 N LYS A 29 SHEET 8 A13 TYR A 192 ASN A 202 -1 N MSE A 198 O LEU A 211 SHEET 9 A13 LEU A 176 TYR A 188 -1 N TYR A 188 O TYR A 192 SHEET 10 A13 PRO A 164 ASP A 171 -1 N PHE A 169 O LEU A 177 SHEET 11 A13 TYR A 150 ASP A 158 -1 N TRP A 156 O LEU A 165 SHEET 12 A13 GLN A 134 PRO A 143 -1 N PHE A 137 O LEU A 157 SHEET 13 A13 TYR A 121 PHE A 131 -1 N GLU A 129 O VAL A 136 LINK NE2 HIS A 125 MG MG A 235 1555 1555 2.00 LINK OD1 ASP A 128 MG MG A 235 1555 1555 2.40 LINK C THR A 23 N MSE A 24 1555 1555 1.33 LINK C MSE A 24 N GLU A 25 1555 1555 1.31 LINK C GLU A 25 N MSE A 26 1555 1555 1.33 LINK C MSE A 26 N ILE A 27 1555 1555 1.33 LINK C LEU A 39 N MSE A 40 1555 1555 1.33 LINK C MSE A 40 N ARG A 41 1555 1555 1.32 LINK C PHE A 103 N AMSE A 104 1555 1555 1.33 LINK C PHE A 103 N BMSE A 104 1555 1555 1.34 LINK C AMSE A 104 N GLY A 105 1555 1555 1.32 LINK C BMSE A 104 N GLY A 105 1555 1555 1.34 LINK C THR A 197 N MSE A 198 1555 1555 1.32 LINK C MSE A 198 N ALA A 199 1555 1555 1.34 LINK C ALA A 199 N MSE A 200 1555 1555 1.34 LINK C MSE A 200 N THR A 201 1555 1555 1.33 CISPEP 1 GLN A 60 PRO A 61 0 -7.12 SITE 1 AC1 4 LYS A 2 HIS A 125 LYS A 127 ASP A 128 CRYST1 48.157 128.874 41.968 90.00 90.00 90.00 P 21 21 2 4 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 0.020765 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007760 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023828 0.00000