HEADER OXIDOREDUCTASE 06-MAY-09 3HCG TITLE STRUCTURE OF THE C-TERMINAL DOMAIN (MSRB) OF NEISSERIA MENINGITIDIS TITLE 2 PILB (REDUCED FORM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE METHIONINE SULFOXIDE REDUCTASE MSRA/MSRB; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: MSRB DOMAIN (UNP RESIDUES 377-522); COMPND 5 SYNONYM: PEPTIDE-METHIONINE (R)-S-OXIDE REDUCTASE; COMPND 6 EC: 1.8.4.12; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEISSERIA MENINGITIDIS SEROGROUP A; SOURCE 3 ORGANISM_TAXID: 65699; SOURCE 4 STRAIN: Z2491; SOURCE 5 GENE: MSRAB, NMA0290, PILB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BE002; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PSKPILBMSRB KEYWDS PILB, METHIONINE SULFOXIDE REDUCTASE B, REDUCED FORM, DISULFIDE BOND, KEYWDS 2 ELECTRON TRANSPORT, MULTIFUNCTIONAL ENZYME, OXIDOREDUCTASE, REDOX- KEYWDS 3 ACTIVE CENTER, TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR F.M.RANAIVOSON,B.KAUFFMANN,F.FAVIER REVDAT 3 16-OCT-24 3HCG 1 REMARK LINK REVDAT 2 09-APR-14 3HCG 1 JRNL VERSN REVDAT 1 13-OCT-09 3HCG 0 JRNL AUTH F.M.RANAIVOSON,F.NEIERS,B.KAUFFMANN,S.BOSCHI-MULLER, JRNL AUTH 2 G.BRANLANT,F.FAVIER JRNL TITL METHIONINE SULFOXIDE REDUCTASE B DISPLAYS A HIGH LEVEL OF JRNL TITL 2 FLEXIBILITY. JRNL REF J.MOL.BIOL. V. 394 83 2009 JRNL REFN ISSN 0022-2836 JRNL PMID 19733575 JRNL DOI 10.1016/J.JMB.2009.08.073 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH B.KAUFFMANN,F.FAVIER,A.OLRY,S.BOSCHI-MULLER,P.CARPENTIER, REMARK 1 AUTH 2 G.BRANLANT,A.AUBRY REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY DIFFRACTION STUDIES OF REMARK 1 TITL 2 THE PEPTIDE METHIONINE SULFOXIDE REDUCTASE B DOMAIN OF REMARK 1 TITL 3 NEISSERIA MENINGITIDIS PILB. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 58 1467 2002 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 12198304 REMARK 1 DOI 10.1107/S0907444902010570 REMARK 2 REMARK 2 RESOLUTION. 1.82 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.82 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.59 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.8 REMARK 3 NUMBER OF REFLECTIONS : 59068 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) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3002 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) : 1.82 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3689 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.60 REMARK 3 BIN R VALUE (WORKING SET) : 0.2510 REMARK 3 BIN FREE R VALUE SET COUNT : 200 REMARK 3 BIN FREE R VALUE : 0.3060 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4566 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 747 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.03 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.140 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.139 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.926 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4803 ; 0.014 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6513 ; 1.407 ; 1.951 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 597 ; 6.088 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 237 ;32.608 ;23.586 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 773 ;13.676 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;16.524 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 657 ; 0.099 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3798 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2627 ; 0.206 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3341 ; 0.313 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 773 ; 0.169 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 70 ; 0.210 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 51 ; 0.257 ; 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): 2942 ; 0.831 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4734 ; 1.437 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1861 ; 2.507 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1779 ; 3.797 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 3HCG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-MAY-09. REMARK 100 THE DEPOSITION ID IS D_1000052964. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791, 0.9796, 0.9765 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62578 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.820 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.82 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.21200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SNB REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0,5M KH2PO4, 0.1M TRIS HCL PH 8 , REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 21.83150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 68.84300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 58.61600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 68.84300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.83150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 58.61600 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 THR A 377 REMARK 465 THR B 377 REMARK 465 LYS B 522 REMARK 465 THR C 377 REMARK 465 LYS C 522 REMARK 465 THR D 377 REMARK 465 LYS D 522 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 OE2 GLU B 392 O HOH B 633 1.80 REMARK 500 NZ LYS B 520 O HOH B 645 2.11 REMARK 500 OD2 ASP C 383 OH TYR C 395 2.12 REMARK 500 O HOH C 548 O HOH C 741 2.13 REMARK 500 O HOH A 637 O HOH A 723 2.13 REMARK 500 O HOH A 90 O HOH A 668 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 617 O HOH A 723 4455 1.67 REMARK 500 O HOH C 147 O HOH D 670 3545 1.92 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 CYS A 495 CB CYS A 495 SG -0.101 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 ARG B 465 NE - CZ - NH2 ANGL. DEV. = -3.1 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 PHE B 415 40.99 -140.65 REMARK 500 PRO B 483 39.50 -91.02 REMARK 500 PRO C 483 31.76 -91.66 REMARK 500 PRO D 483 27.65 -79.15 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 TYR D 378 LYS D 379 -143.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 D 1002 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3HCH RELATED DB: PDB REMARK 900 RELATED ID: 3HCI RELATED DB: PDB REMARK 900 RELATED ID: 3HCJ RELATED DB: PDB DBREF 3HCG A 377 522 UNP Q9JWM8 MSRAB_NEIMA 377 522 DBREF 3HCG B 377 522 UNP Q9JWM8 MSRAB_NEIMA 377 522 DBREF 3HCG C 377 522 UNP Q9JWM8 MSRAB_NEIMA 377 522 DBREF 3HCG D 377 522 UNP Q9JWM8 MSRAB_NEIMA 377 522 SEQRES 1 A 146 THR TYR LYS LYS PRO SER ASP ALA GLU LEU LYS ARG THR SEQRES 2 A 146 LEU THR GLU GLU GLN TYR GLN VAL THR GLN ASN SER ALA SEQRES 3 A 146 THR GLU TYR ALA PHE SER HIS GLU TYR ASP HIS LEU PHE SEQRES 4 A 146 LYS PRO GLY ILE TYR VAL ASP VAL VAL SER GLY GLU PRO SEQRES 5 A 146 LEU PHE SER SER ALA ASP LYS TYR ASP SER GLY CYS GLY SEQRES 6 A 146 TRP PRO SER PHE THR ARG PRO ILE ASP ALA LYS SER VAL SEQRES 7 A 146 THR GLU HIS ASP ASP PHE SER TYR ASN MSE ARG ARG THR SEQRES 8 A 146 GLU VAL ARG SER HIS ALA ALA ASP SER HIS LEU GLY HIS SEQRES 9 A 146 VAL PHE PRO ASP GLY PRO ARG ASP LYS GLY GLY LEU ARG SEQRES 10 A 146 TYR CYS ILE ASN GLY ALA SER LEU LYS PHE ILE PRO LEU SEQRES 11 A 146 GLU GLN MSE ASP ALA ALA GLY TYR GLY ALA LEU LYS SER SEQRES 12 A 146 LYS VAL LYS SEQRES 1 B 146 THR TYR LYS LYS PRO SER ASP ALA GLU LEU LYS ARG THR SEQRES 2 B 146 LEU THR GLU GLU GLN TYR GLN VAL THR GLN ASN SER ALA SEQRES 3 B 146 THR GLU TYR ALA PHE SER HIS GLU TYR ASP HIS LEU PHE SEQRES 4 B 146 LYS PRO GLY ILE TYR VAL ASP VAL VAL SER GLY GLU PRO SEQRES 5 B 146 LEU PHE SER SER ALA ASP LYS TYR ASP SER GLY CYS GLY SEQRES 6 B 146 TRP PRO SER PHE THR ARG PRO ILE ASP ALA LYS SER VAL SEQRES 7 B 146 THR GLU HIS ASP ASP PHE SER TYR ASN MSE ARG ARG THR SEQRES 8 B 146 GLU VAL ARG SER HIS ALA ALA ASP SER HIS LEU GLY HIS SEQRES 9 B 146 VAL PHE PRO ASP GLY PRO ARG ASP LYS GLY GLY LEU ARG SEQRES 10 B 146 TYR CYS ILE ASN GLY ALA SER LEU LYS PHE ILE PRO LEU SEQRES 11 B 146 GLU GLN MSE ASP ALA ALA GLY TYR GLY ALA LEU LYS SER SEQRES 12 B 146 LYS VAL LYS SEQRES 1 C 146 THR TYR LYS LYS PRO SER ASP ALA GLU LEU LYS ARG THR SEQRES 2 C 146 LEU THR GLU GLU GLN TYR GLN VAL THR GLN ASN SER ALA SEQRES 3 C 146 THR GLU TYR ALA PHE SER HIS GLU TYR ASP HIS LEU PHE SEQRES 4 C 146 LYS PRO GLY ILE TYR VAL ASP VAL VAL SER GLY GLU PRO SEQRES 5 C 146 LEU PHE SER SER ALA ASP LYS TYR ASP SER GLY CYS GLY SEQRES 6 C 146 TRP PRO SER PHE THR ARG PRO ILE ASP ALA LYS SER VAL SEQRES 7 C 146 THR GLU HIS ASP ASP PHE SER TYR ASN MSE ARG ARG THR SEQRES 8 C 146 GLU VAL ARG SER HIS ALA ALA ASP SER HIS LEU GLY HIS SEQRES 9 C 146 VAL PHE PRO ASP GLY PRO ARG ASP LYS GLY GLY LEU ARG SEQRES 10 C 146 TYR CYS ILE ASN GLY ALA SER LEU LYS PHE ILE PRO LEU SEQRES 11 C 146 GLU GLN MSE ASP ALA ALA GLY TYR GLY ALA LEU LYS SER SEQRES 12 C 146 LYS VAL LYS SEQRES 1 D 146 THR TYR LYS LYS PRO SER ASP ALA GLU LEU LYS ARG THR SEQRES 2 D 146 LEU THR GLU GLU GLN TYR GLN VAL THR GLN ASN SER ALA SEQRES 3 D 146 THR GLU TYR ALA PHE SER HIS GLU TYR ASP HIS LEU PHE SEQRES 4 D 146 LYS PRO GLY ILE TYR VAL ASP VAL VAL SER GLY GLU PRO SEQRES 5 D 146 LEU PHE SER SER ALA ASP LYS TYR ASP SER GLY CYS GLY SEQRES 6 D 146 TRP PRO SER PHE THR ARG PRO ILE ASP ALA LYS SER VAL SEQRES 7 D 146 THR GLU HIS ASP ASP PHE SER TYR ASN MSE ARG ARG THR SEQRES 8 D 146 GLU VAL ARG SER HIS ALA ALA ASP SER HIS LEU GLY HIS SEQRES 9 D 146 VAL PHE PRO ASP GLY PRO ARG ASP LYS GLY GLY LEU ARG SEQRES 10 D 146 TYR CYS ILE ASN GLY ALA SER LEU LYS PHE ILE PRO LEU SEQRES 11 D 146 GLU GLN MSE ASP ALA ALA GLY TYR GLY ALA LEU LYS SER SEQRES 12 D 146 LYS VAL LYS MODRES 3HCG MSE A 464 MET SELENOMETHIONINE MODRES 3HCG MSE A 509 MET SELENOMETHIONINE MODRES 3HCG MSE B 464 MET SELENOMETHIONINE MODRES 3HCG MSE B 509 MET SELENOMETHIONINE MODRES 3HCG MSE C 464 MET SELENOMETHIONINE MODRES 3HCG MSE C 509 MET SELENOMETHIONINE MODRES 3HCG MSE D 464 MET SELENOMETHIONINE MODRES 3HCG MSE D 509 MET SELENOMETHIONINE HET MSE A 464 8 HET MSE A 509 8 HET MSE B 464 8 HET MSE B 509 8 HET MSE C 464 8 HET MSE C 509 8 HET MSE D 464 8 HET MSE D 509 8 HET PO4 A1003 5 HET PO4 B1001 5 HET PO4 D1002 5 HETNAM MSE SELENOMETHIONINE HETNAM PO4 PHOSPHATE ION FORMUL 1 MSE 8(C5 H11 N O2 SE) FORMUL 5 PO4 3(O4 P 3-) FORMUL 8 HOH *747(H2 O) HELIX 1 1 SER A 382 LEU A 390 1 9 HELIX 2 2 THR A 391 SER A 401 1 11 HELIX 3 3 HIS A 409 LEU A 414 5 6 HELIX 4 4 ASP A 450 LYS A 452 5 3 HELIX 5 5 PRO A 486 GLY A 490 5 5 HELIX 6 6 GLN A 508 GLY A 513 1 6 HELIX 7 7 TYR A 514 VAL A 521 5 8 HELIX 8 8 SER B 382 LEU B 390 1 9 HELIX 9 9 THR B 391 SER B 401 1 11 HELIX 10 10 HIS B 409 LEU B 414 5 6 HELIX 11 11 ASP B 450 LYS B 452 5 3 HELIX 12 12 PHE B 460 MSE B 464 5 5 HELIX 13 13 PRO B 486 GLY B 490 5 5 HELIX 14 14 GLU B 507 MSE B 509 5 3 HELIX 15 15 TYR B 514 VAL B 521 5 8 HELIX 16 16 SER C 382 LEU C 390 1 9 HELIX 17 17 THR C 391 SER C 401 1 11 HELIX 18 18 ASP C 450 LYS C 452 5 3 HELIX 19 19 PHE C 460 MSE C 464 5 5 HELIX 20 20 PRO C 486 GLY C 490 5 5 HELIX 21 21 GLN C 508 GLY C 513 1 6 HELIX 22 22 TYR C 514 VAL C 521 5 8 HELIX 23 23 SER D 382 LEU D 390 1 9 HELIX 24 24 THR D 391 SER D 401 1 11 HELIX 25 25 HIS D 409 LEU D 414 5 6 HELIX 26 26 ALA D 433 LYS D 435 5 3 HELIX 27 27 ASP D 450 LYS D 452 5 3 HELIX 28 28 GLN D 508 GLY D 513 1 6 HELIX 29 29 TYR D 514 VAL D 521 5 8 SHEET 1 A 3 PRO A 428 SER A 431 0 SHEET 2 A 3 GLY A 418 ASP A 422 -1 N TYR A 420 O PHE A 430 SHEET 3 A 3 LEU A 501 PRO A 505 -1 O ILE A 504 N ILE A 419 SHEET 1 B 6 LYS A 435 TYR A 436 0 SHEET 2 B 6 SER A 444 PHE A 445 -1 O SER A 444 N TYR A 436 SHEET 3 B 6 ARG A 493 ILE A 496 -1 O TYR A 494 N PHE A 445 SHEET 4 B 6 HIS A 477 PHE A 482 -1 N HIS A 480 O CYS A 495 SHEET 5 B 6 MSE A 464 SER A 471 -1 N VAL A 469 O LEU A 478 SHEET 6 B 6 VAL A 454 SER A 461 -1 N HIS A 457 O GLU A 468 SHEET 1 C 3 PRO B 428 SER B 431 0 SHEET 2 C 3 GLY B 418 ASP B 422 -1 N TYR B 420 O PHE B 430 SHEET 3 C 3 LEU B 501 PRO B 505 -1 O ILE B 504 N ILE B 419 SHEET 1 D 6 LYS B 435 TYR B 436 0 SHEET 2 D 6 SER B 444 PHE B 445 -1 O SER B 444 N TYR B 436 SHEET 3 D 6 ARG B 493 ILE B 496 -1 O TYR B 494 N PHE B 445 SHEET 4 D 6 HIS B 477 PHE B 482 -1 N HIS B 480 O CYS B 495 SHEET 5 D 6 ARG B 466 SER B 471 -1 N VAL B 469 O LEU B 478 SHEET 6 D 6 VAL B 454 ASP B 459 -1 N HIS B 457 O GLU B 468 SHEET 1 E 3 PRO C 428 SER C 431 0 SHEET 2 E 3 GLY C 418 ASP C 422 -1 N TYR C 420 O PHE C 430 SHEET 3 E 3 LEU C 501 PRO C 505 -1 O ILE C 504 N ILE C 419 SHEET 1 F 6 LYS C 435 TYR C 436 0 SHEET 2 F 6 SER C 444 PHE C 445 -1 O SER C 444 N TYR C 436 SHEET 3 F 6 ARG C 493 ILE C 496 -1 O TYR C 494 N PHE C 445 SHEET 4 F 6 HIS C 477 PHE C 482 -1 N HIS C 480 O CYS C 495 SHEET 5 F 6 ARG C 466 SER C 471 -1 N VAL C 469 O GLY C 479 SHEET 6 F 6 VAL C 454 ASP C 459 -1 N HIS C 457 O GLU C 468 SHEET 1 G 3 PRO D 428 SER D 431 0 SHEET 2 G 3 GLY D 418 ASP D 422 -1 N TYR D 420 O PHE D 430 SHEET 3 G 3 LEU D 501 PRO D 505 -1 O ILE D 504 N ILE D 419 SHEET 1 H 5 SER D 444 PHE D 445 0 SHEET 2 H 5 ARG D 493 ILE D 496 -1 O TYR D 494 N PHE D 445 SHEET 3 H 5 HIS D 477 PHE D 482 -1 N HIS D 480 O CYS D 495 SHEET 4 H 5 MSE D 464 SER D 471 -1 N VAL D 469 O GLY D 479 SHEET 5 H 5 VAL D 454 SER D 461 -1 N HIS D 457 O GLU D 468 SSBOND 1 CYS A 440 CYS A 495 1555 1555 2.87 LINK C ASN A 463 N MSE A 464 1555 1555 1.33 LINK C MSE A 464 N ARG A 465 1555 1555 1.32 LINK C GLN A 508 N MSE A 509 1555 1555 1.33 LINK C MSE A 509 N ASP A 510 1555 1555 1.32 LINK C ASN B 463 N MSE B 464 1555 1555 1.32 LINK C MSE B 464 N ARG B 465 1555 1555 1.32 LINK C GLN B 508 N MSE B 509 1555 1555 1.33 LINK C MSE B 509 N ASP B 510 1555 1555 1.33 LINK C ASN C 463 N MSE C 464 1555 1555 1.32 LINK C MSE C 464 N ARG C 465 1555 1555 1.32 LINK C GLN C 508 N MSE C 509 1555 1555 1.32 LINK C MSE C 509 N ASP C 510 1555 1555 1.33 LINK C ASN D 463 N MSE D 464 1555 1555 1.33 LINK C MSE D 464 N ARG D 465 1555 1555 1.32 LINK C GLN D 508 N MSE D 509 1555 1555 1.33 LINK C MSE D 509 N ASP D 510 1555 1555 1.33 SITE 1 AC1 11 HOH A 33 HOH A 203 HOH A 360 SER A 401 SITE 2 AC1 11 ASP A 459 ARG A 466 GLU A 468 HIS A 477 SITE 3 AC1 11 HIS A 480 HOH A 634 TYR C 462 SITE 1 AC2 4 ARG A 388 GLU B 393 GLU B 404 TYR B 405 SITE 1 AC3 8 TYR B 462 HOH D 25 HOH D 136 ASP D 459 SITE 2 AC3 8 ARG D 466 HIS D 477 HIS D 480 HOH D 565 CRYST1 43.663 117.232 137.686 90.00 90.00 90.00 P 21 21 21 16 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 0.022903 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008530 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007263 0.00000