HEADER PENICILLIN-BINDING PROTEIN 25-APR-12 3VSK TITLE CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 3 (PBP3) FROM TITLE 2 METHICILIN-RESISTANT STAPHYLOCOCCUS AUREUS IN THE APO FORM. COMPND MOL_ID: 1; COMPND 2 MOLECULE: PENICILLIN-BINDING PROTEIN 3; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 46-691; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 196620; SOURCE 4 STRAIN: MW2; SOURCE 5 GENE: PBP3, MW1504; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS PENICILLIN-BINDING DOMAIN, TRANSPEPTIDASE, PENICILLIN-BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.YOSHIDA,J.R.TAME,S.Y.PARK REVDAT 2 20-MAR-24 3VSK 1 REMARK REVDAT 1 31-OCT-12 3VSK 0 JRNL AUTH H.YOSHIDA,F.KAWAI,E.OBAYASHI,S.AKASHI,D.I.ROPER,J.R.TAME, JRNL AUTH 2 S.Y.PARK JRNL TITL CRYSTAL STRUCTURES OF PENICILLIN-BINDING PROTEIN 3 (PBP3) JRNL TITL 2 FROM METHICILLIN-RESISTANT STAPHYLOCOCCUS AUREUS IN THE APO JRNL TITL 3 AND CEFOTAXIME-BOUND FORMS. JRNL REF J.MOL.BIOL. V. 423 351 2012 JRNL REFN ISSN 0022-2836 JRNL PMID 22846910 JRNL DOI 10.1016/J.JMB.2012.07.012 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.2_869) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 85097 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.263 REMARK 3 R VALUE (WORKING SET) : 0.261 REMARK 3 FREE R VALUE : 0.300 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 4274 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 40.9090 - 7.1362 0.98 2987 161 0.2430 0.2375 REMARK 3 2 7.1362 - 5.6691 0.99 2875 136 0.2619 0.2985 REMARK 3 3 5.6691 - 4.9538 0.99 2802 166 0.2383 0.3028 REMARK 3 4 4.9538 - 4.5015 0.99 2821 140 0.1939 0.2328 REMARK 3 5 4.5015 - 4.1792 0.99 2809 146 0.1975 0.2626 REMARK 3 6 4.1792 - 3.9330 0.99 2778 152 0.2135 0.2695 REMARK 3 7 3.9330 - 3.7362 0.99 2782 144 0.2192 0.2644 REMARK 3 8 3.7362 - 3.5737 0.99 2760 151 0.2362 0.2614 REMARK 3 9 3.5737 - 3.4362 0.99 2753 155 0.2487 0.3219 REMARK 3 10 3.4362 - 3.3176 0.99 2782 145 0.2610 0.3235 REMARK 3 11 3.3176 - 3.2139 0.99 2719 162 0.2773 0.3158 REMARK 3 12 3.2139 - 3.1221 0.99 2750 149 0.2691 0.2772 REMARK 3 13 3.1221 - 3.0399 0.99 2750 159 0.2728 0.3406 REMARK 3 14 3.0399 - 2.9658 0.99 2719 148 0.2777 0.3143 REMARK 3 15 2.9658 - 2.8984 0.99 2745 131 0.2885 0.3795 REMARK 3 16 2.8984 - 2.8367 0.98 2700 152 0.3104 0.3599 REMARK 3 17 2.8367 - 2.7800 0.98 2695 137 0.3045 0.3289 REMARK 3 18 2.7800 - 2.7275 0.98 2706 143 0.3070 0.3591 REMARK 3 19 2.7275 - 2.6788 0.98 2706 131 0.3028 0.3702 REMARK 3 20 2.6788 - 2.6334 0.96 2641 140 0.3098 0.3447 REMARK 3 21 2.6334 - 2.5910 0.96 2689 117 0.3113 0.3465 REMARK 3 22 2.5910 - 2.5511 0.95 2592 153 0.3145 0.3865 REMARK 3 23 2.5511 - 2.5136 0.95 2607 130 0.3299 0.3604 REMARK 3 24 2.5136 - 2.4782 0.94 2551 161 0.3359 0.3508 REMARK 3 25 2.4782 - 2.4447 0.95 2606 152 0.3347 0.3564 REMARK 3 26 2.4447 - 2.4130 0.93 2570 116 0.3473 0.3929 REMARK 3 27 2.4130 - 2.3828 0.93 2552 135 0.3658 0.3991 REMARK 3 28 2.3828 - 2.3541 0.91 2461 134 0.3785 0.3622 REMARK 3 29 2.3541 - 2.3267 0.89 2483 107 0.3946 0.4054 REMARK 3 30 2.3267 - 2.3006 0.88 2432 121 0.4051 0.4055 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.60 REMARK 3 K_SOL : 0.35 REMARK 3 B_SOL : 65.65 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.790 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.900 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.28610 REMARK 3 B22 (A**2) : 0.28610 REMARK 3 B33 (A**2) : -0.97640 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.010 10053 REMARK 3 ANGLE : 1.461 13541 REMARK 3 CHIRALITY : 0.107 1499 REMARK 3 PLANARITY : 0.007 1756 REMARK 3 DIHEDRAL : 21.295 3883 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3VSK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-MAY-12. REMARK 100 THE DEPOSITION ID IS D_1000095447. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-FEB-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : SI 111 REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 85132 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.49400 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: MIR REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0M AMMONIUM SULFATE, 0.5M LITHIUM REMARK 280 CHLORIDE, 5% GLYCEROL, PH 8.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 94.67950 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 71.70950 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 71.70950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 142.01925 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 71.70950 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 71.70950 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 47.33975 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 71.70950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 71.70950 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 142.01925 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 71.70950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 71.70950 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 47.33975 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 94.67950 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 54780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 ASN A 627 REMARK 465 GLY A 628 REMARK 465 GLN A 679 REMARK 465 LEU A 680 REMARK 465 GLY A 681 REMARK 465 LYS A 682 REMARK 465 ASP A 683 REMARK 465 ASP A 684 REMARK 465 LYS A 685 REMARK 465 ASN A 686 REMARK 465 LYS A 687 REMARK 465 ASP A 688 REMARK 465 LYS A 689 REMARK 465 ASP A 690 REMARK 465 LYS A 691 REMARK 465 GLY B 602 REMARK 465 GLY B 628 REMARK 465 GLN B 679 REMARK 465 LEU B 680 REMARK 465 GLY B 681 REMARK 465 LYS B 682 REMARK 465 ASP B 683 REMARK 465 ASP B 684 REMARK 465 LYS B 685 REMARK 465 ASN B 686 REMARK 465 LYS B 687 REMARK 465 ASP B 688 REMARK 465 LYS B 689 REMARK 465 ASP B 690 REMARK 465 LYS B 691 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 PRO B 641 C - N - CD ANGL. DEV. = -12.8 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 LYS A 52 -43.43 -131.91 REMARK 500 ASN A 57 -96.03 -90.89 REMARK 500 ASP A 58 -85.89 -111.45 REMARK 500 ASP A 82 -167.45 -122.59 REMARK 500 SER A 152 -94.31 -50.32 REMARK 500 ARG A 167 -87.85 -145.43 REMARK 500 SER A 175 86.01 -41.86 REMARK 500 LEU A 194 -8.71 -155.27 REMARK 500 TYR A 275 -115.57 -148.13 REMARK 500 ASP A 282 -63.14 -23.98 REMARK 500 GLN A 342 37.77 -71.69 REMARK 500 ASN A 359 14.67 -142.60 REMARK 500 ALA A 364 117.21 -174.16 REMARK 500 ASN A 371 -174.99 -60.41 REMARK 500 LYS A 372 31.85 75.51 REMARK 500 SER A 373 -70.82 174.26 REMARK 500 ASP A 380 -67.21 -27.48 REMARK 500 LYS A 406 46.01 -80.60 REMARK 500 GLN A 422 82.11 -66.24 REMARK 500 TYR A 430 0.83 -156.90 REMARK 500 LYS A 433 -78.47 -108.02 REMARK 500 ASN A 434 -141.07 -125.05 REMARK 500 SER A 438 -167.34 -75.34 REMARK 500 ILE A 439 178.28 173.83 REMARK 500 ASP A 498 62.95 -69.34 REMARK 500 THR A 511 -53.01 -120.32 REMARK 500 TYR A 525 -88.96 -111.98 REMARK 500 LEU A 553 -68.69 -99.86 REMARK 500 HIS A 556 -147.66 -105.44 REMARK 500 SER A 558 139.58 -39.95 REMARK 500 LYS A 561 -65.66 -109.86 REMARK 500 GLU A 563 32.00 -76.71 REMARK 500 VAL A 564 143.44 178.47 REMARK 500 ASN A 577 170.81 175.72 REMARK 500 VAL A 606 24.59 -78.06 REMARK 500 SER A 607 -39.02 -138.21 REMARK 500 LYS A 609 -60.03 -12.38 REMARK 500 THR A 611 -152.40 -155.99 REMARK 500 ARG A 631 -163.87 -123.03 REMARK 500 ASP A 644 74.67 -153.97 REMARK 500 LYS A 646 -4.18 -145.19 REMARK 500 PRO A 661 -0.60 -53.27 REMARK 500 TRP A 662 -85.36 -115.96 REMARK 500 PHE A 677 47.10 -101.48 REMARK 500 ASP B 74 -168.11 -74.49 REMARK 500 ASP B 82 -168.76 -117.40 REMARK 500 THR B 98 -104.51 -73.53 REMARK 500 GLN B 99 -25.76 -174.19 REMARK 500 PHE B 128 24.39 -67.16 REMARK 500 LEU B 132 52.10 -101.11 REMARK 500 REMARK 500 THIS ENTRY HAS 100 RAMACHANDRAN OUTLIERS. 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 GLY A 251 ILE A 252 146.80 REMARK 500 ASN A 371 LYS A 372 -143.93 REMARK 500 TYR A 430 PHE A 431 145.51 REMARK 500 ASN A 434 GLY A 435 -145.71 REMARK 500 GLU A 563 VAL A 564 136.51 REMARK 500 PRO A 657 VAL A 658 -145.60 REMARK 500 VAL A 658 PRO A 659 149.92 REMARK 500 PRO A 660 PRO A 661 -146.94 REMARK 500 LYS B 96 THR B 97 -146.93 REMARK 500 LEU B 132 HIS B 133 140.02 REMARK 500 HIS B 133 PRO B 134 147.82 REMARK 500 LYS B 218 LEU B 219 139.05 REMARK 500 LEU B 219 PRO B 220 -149.10 REMARK 500 LYS B 345 ASP B 346 134.17 REMARK 500 ASP B 346 MET B 347 144.28 REMARK 500 ASN B 371 LYS B 372 -148.95 REMARK 500 LYS B 372 SER B 373 147.20 REMARK 500 GLU B 412 THR B 413 -148.80 REMARK 500 LEU B 425 THR B 426 -142.90 REMARK 500 ARG B 428 SER B 429 -148.93 REMARK 500 ASN B 560 LYS B 561 125.31 REMARK 500 LYS B 561 ASP B 562 -138.97 REMARK 500 ASP B 562 GLU B 563 142.84 REMARK 500 VAL B 612 VAL B 613 -137.30 REMARK 500 THR B 621 ALA B 622 -145.36 REMARK 500 VAL B 624 PHE B 625 149.36 REMARK 500 ALA B 640 PRO B 641 -132.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VSL RELATED DB: PDB DBREF 3VSK A 46 691 UNP Q8NWC2 Q8NWC2_STAAW 46 691 DBREF 3VSK B 46 691 UNP Q8NWC2 Q8NWC2_STAAW 46 691 SEQRES 1 A 646 ALA GLN GLY SER HIS TYR LYS GLN ILE ILE LYS ASN ASP SEQRES 2 A 646 GLU ASN ILE THR VAL ASN GLU SER VAL PRO ARG GLY ARG SEQRES 3 A 646 ILE LEU ASP ARG ASN GLY LYS VAL LEU VAL ASP ASN ALA SEQRES 4 A 646 SER LYS MET ALA ILE THR TYR THR ARG GLY ARG LYS THR SEQRES 5 A 646 THR GLN SER GLU MET LEU ASP THR ALA GLU LYS LEU SER SEQRES 6 A 646 LYS LEU ILE LYS MET ASP THR LYS LYS ILE THR GLU ARG SEQRES 7 A 646 ASP LYS LYS ASP PHE TRP ILE GLN LEU HIS PRO LYS LYS SEQRES 8 A 646 ALA LYS ALA MET MET THR LYS GLU GLN ALA MET LEU ALA SEQRES 9 A 646 ASP GLY SER ILE LYS GLN ASP GLN TYR ASP LYS GLN LEU SEQRES 10 A 646 LEU SER LYS ILE ARG LYS SER GLN LEU ASP GLU LEU SER SEQRES 11 A 646 SER LYS ASP LEU GLN VAL LEU ALA ILE PHE ARG GLU MET SEQRES 12 A 646 ASN ALA GLY THR VAL LEU ASP PRO GLN MET ILE LYS ASN SEQRES 13 A 646 GLU ASP VAL SER GLU LYS GLU TYR ALA ALA VAL SER GLN SEQRES 14 A 646 GLN LEU SER LYS LEU PRO GLY VAL ASN THR SER MET ASP SEQRES 15 A 646 TRP ASP ARG LYS TYR PRO TYR GLY ASP THR LEU ARG GLY SEQRES 16 A 646 ILE PHE GLY ASP VAL SER THR PRO ALA GLU GLY ILE PRO SEQRES 17 A 646 LYS GLU LEU THR GLU HIS TYR LEU SER LYS GLY TYR SER SEQRES 18 A 646 ARG ASN ASP ARG VAL GLY LYS SER TYR LEU GLU TYR GLN SEQRES 19 A 646 TYR GLU ASP VAL LEU ARG GLY LYS LYS LYS GLU MET LYS SEQRES 20 A 646 TYR THR THR ASP LYS SER GLY LYS VAL THR SER SER GLU SEQRES 21 A 646 VAL LEU ASN PRO GLY ALA ARG GLY GLN ASP LEU LYS LEU SEQRES 22 A 646 THR ILE ASP ILE ASP LEU GLN LYS GLU VAL GLU ALA LEU SEQRES 23 A 646 LEU ASP LYS GLN ILE LYS LYS LEU ARG SER GLN GLY ALA SEQRES 24 A 646 LYS ASP MET ASP ASN ALA MET MET VAL VAL GLN ASN PRO SEQRES 25 A 646 LYS ASN GLY ASP ILE LEU ALA LEU ALA GLY LYS GLN ILE SEQRES 26 A 646 ASN LYS SER GLY LYS MET THR ASP TYR ASP ILE GLY THR SEQRES 27 A 646 PHE THR SER GLN PHE ALA VAL GLY SER SER VAL LYS GLY SEQRES 28 A 646 GLY THR LEU LEU ALA GLY TYR GLN ASN LYS ALA ILE LYS SEQRES 29 A 646 VAL GLY GLU THR MET VAL ASP GLU PRO LEU HIS PHE GLN SEQRES 30 A 646 GLY GLY LEU THR LYS ARG SER TYR PHE ASN LYS ASN GLY SEQRES 31 A 646 HIS VAL SER ILE ASN ASP LYS GLN ALA LEU MET HIS SER SEQRES 32 A 646 SER ASN VAL TYR MET PHE LYS THR ALA LEU LYS LEU ALA SEQRES 33 A 646 GLY ASP PRO TYR TYR SER GLY MET ALA LEU PRO SER ASP SEQRES 34 A 646 ILE SER SER PRO ALA GLN LYS LEU ARG ARG GLY LEU ASN SEQRES 35 A 646 GLN VAL GLY LEU GLY VAL LYS THR GLY ILE ASP LEU PRO SEQRES 36 A 646 ASN GLU THR ARG GLY GLN ILE GLU PRO LEU THR ASN ASN SEQRES 37 A 646 PRO GLY ASN TYR LEU ASP LEU SER ILE GLY GLN TYR ASP SEQRES 38 A 646 THR TYR THR PRO LEU GLN LEU SER GLN TYR VAL SER THR SEQRES 39 A 646 ILE ALA ASN ASP GLY TYR ARG ILE GLN PRO HIS ILE GLY SEQRES 40 A 646 LEU THR ILE HIS GLU SER THR ASN LYS ASP GLU VAL GLY SEQRES 41 A 646 PRO LEU LYS LYS LYS ILE ASN GLY THR VAL LEU ASN LYS SEQRES 42 A 646 VAL ASN ASN THR GLU LYS GLU ILE LYS GLN ILE GLN GLU SEQRES 43 A 646 GLY PHE LYS MET ALA PHE ASN ASP LYS ASP GLY THR GLY SEQRES 44 A 646 TYR VAL SER PHE LYS ASP THR VAL VAL PRO THR ALA GLY SEQRES 45 A 646 LYS THR GLY THR ALA GLU VAL PHE GLN ASN GLY GLU PRO SEQRES 46 A 646 ARG VAL ASN SER THR TYR ILE GLY TYR ALA PRO ILE ASP SEQRES 47 A 646 ASP PRO LYS LEU ALA PHE SER ILE VAL TYR THR ASN GLN SEQRES 48 A 646 PRO VAL PRO PRO PRO TRP LEU THR GLY GLY ASP LEU GLY SEQRES 49 A 646 ARG ASP VAL ILE ASN TYR TYR PHE LYS GLN LEU GLY LYS SEQRES 50 A 646 ASP ASP LYS ASN LYS ASP LYS ASP LYS SEQRES 1 B 646 ALA GLN GLY SER HIS TYR LYS GLN ILE ILE LYS ASN ASP SEQRES 2 B 646 GLU ASN ILE THR VAL ASN GLU SER VAL PRO ARG GLY ARG SEQRES 3 B 646 ILE LEU ASP ARG ASN GLY LYS VAL LEU VAL ASP ASN ALA SEQRES 4 B 646 SER LYS MET ALA ILE THR TYR THR ARG GLY ARG LYS THR SEQRES 5 B 646 THR GLN SER GLU MET LEU ASP THR ALA GLU LYS LEU SER SEQRES 6 B 646 LYS LEU ILE LYS MET ASP THR LYS LYS ILE THR GLU ARG SEQRES 7 B 646 ASP LYS LYS ASP PHE TRP ILE GLN LEU HIS PRO LYS LYS SEQRES 8 B 646 ALA LYS ALA MET MET THR LYS GLU GLN ALA MET LEU ALA SEQRES 9 B 646 ASP GLY SER ILE LYS GLN ASP GLN TYR ASP LYS GLN LEU SEQRES 10 B 646 LEU SER LYS ILE ARG LYS SER GLN LEU ASP GLU LEU SER SEQRES 11 B 646 SER LYS ASP LEU GLN VAL LEU ALA ILE PHE ARG GLU MET SEQRES 12 B 646 ASN ALA GLY THR VAL LEU ASP PRO GLN MET ILE LYS ASN SEQRES 13 B 646 GLU ASP VAL SER GLU LYS GLU TYR ALA ALA VAL SER GLN SEQRES 14 B 646 GLN LEU SER LYS LEU PRO GLY VAL ASN THR SER MET ASP SEQRES 15 B 646 TRP ASP ARG LYS TYR PRO TYR GLY ASP THR LEU ARG GLY SEQRES 16 B 646 ILE PHE GLY ASP VAL SER THR PRO ALA GLU GLY ILE PRO SEQRES 17 B 646 LYS GLU LEU THR GLU HIS TYR LEU SER LYS GLY TYR SER SEQRES 18 B 646 ARG ASN ASP ARG VAL GLY LYS SER TYR LEU GLU TYR GLN SEQRES 19 B 646 TYR GLU ASP VAL LEU ARG GLY LYS LYS LYS GLU MET LYS SEQRES 20 B 646 TYR THR THR ASP LYS SER GLY LYS VAL THR SER SER GLU SEQRES 21 B 646 VAL LEU ASN PRO GLY ALA ARG GLY GLN ASP LEU LYS LEU SEQRES 22 B 646 THR ILE ASP ILE ASP LEU GLN LYS GLU VAL GLU ALA LEU SEQRES 23 B 646 LEU ASP LYS GLN ILE LYS LYS LEU ARG SER GLN GLY ALA SEQRES 24 B 646 LYS ASP MET ASP ASN ALA MET MET VAL VAL GLN ASN PRO SEQRES 25 B 646 LYS ASN GLY ASP ILE LEU ALA LEU ALA GLY LYS GLN ILE SEQRES 26 B 646 ASN LYS SER GLY LYS MET THR ASP TYR ASP ILE GLY THR SEQRES 27 B 646 PHE THR SER GLN PHE ALA VAL GLY SER SER VAL LYS GLY SEQRES 28 B 646 GLY THR LEU LEU ALA GLY TYR GLN ASN LYS ALA ILE LYS SEQRES 29 B 646 VAL GLY GLU THR MET VAL ASP GLU PRO LEU HIS PHE GLN SEQRES 30 B 646 GLY GLY LEU THR LYS ARG SER TYR PHE ASN LYS ASN GLY SEQRES 31 B 646 HIS VAL SER ILE ASN ASP LYS GLN ALA LEU MET HIS SER SEQRES 32 B 646 SER ASN VAL TYR MET PHE LYS THR ALA LEU LYS LEU ALA SEQRES 33 B 646 GLY ASP PRO TYR TYR SER GLY MET ALA LEU PRO SER ASP SEQRES 34 B 646 ILE SER SER PRO ALA GLN LYS LEU ARG ARG GLY LEU ASN SEQRES 35 B 646 GLN VAL GLY LEU GLY VAL LYS THR GLY ILE ASP LEU PRO SEQRES 36 B 646 ASN GLU THR ARG GLY GLN ILE GLU PRO LEU THR ASN ASN SEQRES 37 B 646 PRO GLY ASN TYR LEU ASP LEU SER ILE GLY GLN TYR ASP SEQRES 38 B 646 THR TYR THR PRO LEU GLN LEU SER GLN TYR VAL SER THR SEQRES 39 B 646 ILE ALA ASN ASP GLY TYR ARG ILE GLN PRO HIS ILE GLY SEQRES 40 B 646 LEU THR ILE HIS GLU SER THR ASN LYS ASP GLU VAL GLY SEQRES 41 B 646 PRO LEU LYS LYS LYS ILE ASN GLY THR VAL LEU ASN LYS SEQRES 42 B 646 VAL ASN ASN THR GLU LYS GLU ILE LYS GLN ILE GLN GLU SEQRES 43 B 646 GLY PHE LYS MET ALA PHE ASN ASP LYS ASP GLY THR GLY SEQRES 44 B 646 TYR VAL SER PHE LYS ASP THR VAL VAL PRO THR ALA GLY SEQRES 45 B 646 LYS THR GLY THR ALA GLU VAL PHE GLN ASN GLY GLU PRO SEQRES 46 B 646 ARG VAL ASN SER THR TYR ILE GLY TYR ALA PRO ILE ASP SEQRES 47 B 646 ASP PRO LYS LEU ALA PHE SER ILE VAL TYR THR ASN GLN SEQRES 48 B 646 PRO VAL PRO PRO PRO TRP LEU THR GLY GLY ASP LEU GLY SEQRES 49 B 646 ARG ASP VAL ILE ASN TYR TYR PHE LYS GLN LEU GLY LYS SEQRES 50 B 646 ASP ASP LYS ASN LYS ASP LYS ASP LYS FORMUL 3 HOH *260(H2 O) HELIX 1 1 THR A 98 ILE A 113 1 16 HELIX 2 2 ASP A 116 ILE A 120 5 5 HELIX 3 3 THR A 121 HIS A 133 1 13 HELIX 4 4 HIS A 133 ALA A 139 1 7 HELIX 5 5 MET A 141 ALA A 149 1 9 HELIX 6 6 LYS A 154 SER A 164 1 11 HELIX 7 7 SER A 169 LEU A 174 5 6 HELIX 8 8 SER A 175 ASN A 189 1 15 HELIX 9 9 SER A 205 LEU A 219 1 15 HELIX 10 10 LEU A 238 GLY A 243 1 6 HELIX 11 11 PRO A 253 GLU A 255 5 3 HELIX 12 12 LEU A 256 SER A 262 1 7 HELIX 13 13 TYR A 275 TYR A 280 1 6 HELIX 14 14 TYR A 280 ARG A 285 1 6 HELIX 15 15 ASP A 321 LEU A 339 1 19 HELIX 16 16 ILE A 381 SER A 386 1 6 HELIX 17 17 GLY A 391 SER A 393 5 3 HELIX 18 18 VAL A 394 ASN A 405 1 12 HELIX 19 19 ASN A 440 SER A 448 1 9 HELIX 20 20 SER A 449 ALA A 461 1 13 HELIX 21 21 ILE A 475 VAL A 489 1 15 HELIX 22 22 ASN A 513 SER A 521 1 9 HELIX 23 23 THR A 529 ASN A 542 1 14 HELIX 24 24 THR A 582 MET A 595 1 14 HELIX 25 25 GLY A 604 LYS A 609 1 6 HELIX 26 26 GLY A 666 PHE A 677 1 12 HELIX 27 27 GLU B 101 ILE B 113 1 13 HELIX 28 28 THR B 121 PHE B 128 1 8 HELIX 29 29 LYS B 136 MET B 141 1 6 HELIX 30 30 MET B 141 ASP B 150 1 10 HELIX 31 31 LYS B 154 ILE B 166 1 13 HELIX 32 32 ARG B 167 ASP B 172 1 6 HELIX 33 33 SER B 175 ALA B 190 1 16 HELIX 34 34 SER B 205 SER B 213 1 9 HELIX 35 35 LEU B 238 GLY B 243 1 6 HELIX 36 36 PRO B 253 GLU B 255 5 3 HELIX 37 37 LEU B 256 SER B 262 1 7 HELIX 38 38 SER B 274 TYR B 280 1 7 HELIX 39 39 TYR B 280 ARG B 285 1 6 HELIX 40 40 ASP B 321 LYS B 338 1 18 HELIX 41 41 ILE B 381 SER B 386 1 6 HELIX 42 42 GLY B 391 SER B 393 5 3 HELIX 43 43 VAL B 394 ASN B 405 1 12 HELIX 44 44 ASN B 440 SER B 448 1 9 HELIX 45 45 SER B 449 ALA B 461 1 13 HELIX 46 46 ILE B 475 VAL B 489 1 15 HELIX 47 47 ASN B 513 ILE B 522 1 10 HELIX 48 48 THR B 529 ASN B 542 1 14 HELIX 49 49 THR B 582 MET B 595 1 14 HELIX 50 50 GLY B 604 LYS B 609 1 6 HELIX 51 51 GLY B 666 LYS B 678 1 13 SHEET 1 A 4 HIS A 50 LYS A 56 0 SHEET 2 A 4 ASN A 60 SER A 66 -1 O ASN A 64 N GLN A 53 SHEET 3 A 4 LYS A 289 THR A 295 -1 O TYR A 293 N ILE A 61 SHEET 4 A 4 VAL A 301 ASN A 308 -1 O THR A 302 N THR A 294 SHEET 1 B 3 PRO A 196 ASP A 203 0 SHEET 2 B 3 VAL A 79 THR A 92 -1 N TYR A 91 O GLN A 197 SHEET 3 B 3 VAL A 222 LYS A 231 -1 O SER A 225 N ALA A 88 SHEET 1 C 6 PRO A 196 ASP A 203 0 SHEET 2 C 6 VAL A 79 THR A 92 -1 N TYR A 91 O GLN A 197 SHEET 3 C 6 ILE A 72 LEU A 73 -1 N ILE A 72 O LEU A 80 SHEET 4 C 6 LEU A 316 LEU A 318 1 O LEU A 318 N LEU A 73 SHEET 5 C 6 GLY A 552 ILE A 555 -1 O THR A 554 N LYS A 317 SHEET 6 C 6 LYS A 569 LYS A 570 -1 O LYS A 569 N ILE A 555 SHEET 1 D 6 LYS A 375 ASP A 378 0 SHEET 2 D 6 ALA A 366 ILE A 370 -1 N LYS A 368 O THR A 377 SHEET 3 D 6 ASN A 349 GLN A 355 -1 N ALA A 350 O GLY A 367 SHEET 4 D 6 LEU A 647 GLN A 656 -1 O ALA A 648 N GLN A 355 SHEET 5 D 6 ARG A 631 ALA A 640 -1 N VAL A 632 O GLN A 656 SHEET 6 D 6 ALA A 616 VAL A 624 -1 N GLY A 620 O THR A 635 SHEET 1 E 2 LEU A 419 HIS A 420 0 SHEET 2 E 2 LEU A 425 THR A 426 -1 O THR A 426 N LEU A 419 SHEET 1 F 2 TYR A 545 ILE A 547 0 SHEET 2 F 2 VAL A 575 LYS A 578 -1 O LEU A 576 N ARG A 546 SHEET 1 G 4 HIS B 50 LYS B 56 0 SHEET 2 G 4 ASN B 60 SER B 66 -1 O ASN B 64 N GLN B 53 SHEET 3 G 4 LYS B 289 THR B 295 -1 O LYS B 289 N GLU B 65 SHEET 4 G 4 VAL B 301 ASN B 308 -1 O THR B 302 N THR B 294 SHEET 1 H 3 GLN B 197 ASP B 203 0 SHEET 2 H 3 VAL B 79 TYR B 91 -1 N MET B 87 O GLU B 202 SHEET 3 H 3 VAL B 222 LYS B 231 -1 O ASP B 227 N LYS B 86 SHEET 1 I 6 GLN B 197 ASP B 203 0 SHEET 2 I 6 VAL B 79 TYR B 91 -1 N MET B 87 O GLU B 202 SHEET 3 I 6 ILE B 72 LEU B 73 -1 N ILE B 72 O LEU B 80 SHEET 4 I 6 ASP B 315 LEU B 318 1 O LEU B 318 N LEU B 73 SHEET 5 I 6 GLY B 552 HIS B 556 -1 O THR B 554 N LYS B 317 SHEET 6 I 6 LEU B 567 LYS B 570 -1 O LYS B 569 N ILE B 555 SHEET 1 J 6 MET B 376 ASP B 378 0 SHEET 2 J 6 ASP B 361 GLN B 369 -1 N LYS B 368 O THR B 377 SHEET 3 J 6 ASN B 349 GLN B 355 -1 N VAL B 354 O LEU B 363 SHEET 4 J 6 ALA B 648 GLN B 656 -1 O ALA B 648 N GLN B 355 SHEET 5 J 6 VAL B 632 TYR B 639 -1 N SER B 634 O TYR B 653 SHEET 6 J 6 ALA B 616 GLY B 620 -1 N ALA B 616 O TYR B 639 SHEET 1 K 2 TYR B 545 ILE B 547 0 SHEET 2 K 2 VAL B 575 LYS B 578 -1 O ASN B 577 N ARG B 546 CISPEP 1 ALA A 640 PRO A 641 0 -8.75 CRYST1 143.419 143.419 189.359 90.00 90.00 90.00 P 43 21 2 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 0.006973 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006973 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005281 0.00000