HEADER PENICILLIN-BINDING PROTEIN 25-APR-12 3VSL TITLE CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 3 (PBP3) FROM TITLE 2 METHICILIN-RESISTANT STAPHYLOCOCCUS AUREUS IN THE CEFOTAXIME BOUND TITLE 3 FORM. CAVEAT 3VSL THE LIGAND CEF HAS WRONG GEOMETRY COMPND MOL_ID: 1; COMPND 2 MOLECULE: PENICILLIN-BINDING PROTEIN 3; COMPND 3 CHAIN: A, B; COMPND 4 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 3 13-NOV-24 3VSL 1 REMARK LINK REVDAT 2 15-MAR-17 3VSL 1 FORMUL HETNAM HETATM REVDAT 1 31-OCT-12 3VSL 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. 2.40 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.440 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 75891 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.250 REMARK 3 R VALUE (WORKING SET) : 0.247 REMARK 3 FREE R VALUE : 0.316 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3797 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 48.8713 - 7.1926 0.99 2959 145 0.2222 0.2881 REMARK 3 2 7.1926 - 5.7118 1.00 2815 146 0.2527 0.3212 REMARK 3 3 5.7118 - 4.9906 1.00 2801 133 0.2306 0.3284 REMARK 3 4 4.9906 - 4.5347 1.00 2752 141 0.1763 0.2720 REMARK 3 5 4.5347 - 4.2099 1.00 2725 145 0.1734 0.2485 REMARK 3 6 4.2099 - 3.9618 1.00 2719 155 0.1883 0.2473 REMARK 3 7 3.9618 - 3.7634 1.00 2711 142 0.1952 0.2573 REMARK 3 8 3.7634 - 3.5997 0.99 2718 143 0.2111 0.3245 REMARK 3 9 3.5997 - 3.4611 1.00 2732 133 0.2277 0.3091 REMARK 3 10 3.4611 - 3.3417 0.99 2696 136 0.2161 0.2772 REMARK 3 11 3.3417 - 3.2373 0.99 2651 172 0.2291 0.2803 REMARK 3 12 3.2373 - 3.1447 0.99 2683 145 0.2462 0.3321 REMARK 3 13 3.1447 - 3.0620 0.99 2666 160 0.2657 0.3481 REMARK 3 14 3.0620 - 2.9873 0.99 2695 117 0.2805 0.3172 REMARK 3 15 2.9873 - 2.9194 0.99 2659 134 0.2885 0.3757 REMARK 3 16 2.9194 - 2.8572 0.99 2664 153 0.3015 0.3394 REMARK 3 17 2.8572 - 2.8001 0.99 2648 152 0.3038 0.4194 REMARK 3 18 2.8001 - 2.7473 0.99 2665 149 0.3101 0.3864 REMARK 3 19 2.7473 - 2.6982 0.99 2628 132 0.3283 0.3582 REMARK 3 20 2.6982 - 2.6525 0.99 2662 138 0.3363 0.3817 REMARK 3 21 2.6525 - 2.6097 0.98 2610 160 0.3365 0.4039 REMARK 3 22 2.6097 - 2.5695 0.98 2663 121 0.3449 0.3787 REMARK 3 23 2.5695 - 2.5317 0.98 2619 147 0.3431 0.3549 REMARK 3 24 2.5317 - 2.4961 0.98 2609 125 0.3355 0.3714 REMARK 3 25 2.4961 - 2.4624 0.94 2528 127 0.3529 0.4043 REMARK 3 26 2.4624 - 2.4304 0.92 2447 125 0.3689 0.3755 REMARK 3 27 2.4304 - 2.4000 0.89 2369 121 0.4031 0.4412 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 : 0.36 REMARK 3 B_SOL : 64.93 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.870 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.220 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 69.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.11370 REMARK 3 B22 (A**2) : -2.11370 REMARK 3 B33 (A**2) : 4.22750 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 10110 REMARK 3 ANGLE : 1.422 13618 REMARK 3 CHIRALITY : 0.104 1513 REMARK 3 PLANARITY : 0.007 1761 REMARK 3 DIHEDRAL : 21.608 3890 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 34.6713 -38.9449 6.6110 REMARK 3 T TENSOR REMARK 3 T11: 0.5895 T22: 0.3966 REMARK 3 T33: 0.1334 T12: 0.1516 REMARK 3 T13: -0.0952 T23: -0.0142 REMARK 3 L TENSOR REMARK 3 L11: 0.5307 L22: 3.6657 REMARK 3 L33: 0.3603 L12: -0.0308 REMARK 3 L13: -0.2450 L23: -0.3140 REMARK 3 S TENSOR REMARK 3 S11: -0.2010 S12: -0.1934 S13: 0.0236 REMARK 3 S21: 0.9208 S22: 0.3517 S23: -0.1619 REMARK 3 S31: -0.0316 S32: 0.0393 S33: -0.0575 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 3VSL 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_1000095448. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-NOV-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 : PHOTON FACTORY REMARK 200 BEAMLINE : BL-1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : SI 111 REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 76011 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.399 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 (%) : 98.2 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.11100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.46000 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.36 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 94.80500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 71.51550 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 71.51550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 142.20750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 71.51550 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 71.51550 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 47.40250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 71.51550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 71.51550 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 142.20750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 71.51550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 71.51550 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 47.40250 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 94.80500 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: 5790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 54380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 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 A 514 C - N - CA ANGL. DEV. = 10.3 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 ASN A 57 -111.57 -100.16 REMARK 500 ASP A 58 -98.24 -91.30 REMARK 500 LYS A 96 70.99 -102.26 REMARK 500 LYS A 111 30.77 -77.54 REMARK 500 LEU A 112 -29.42 -149.67 REMARK 500 THR A 117 -81.94 -66.43 REMARK 500 LYS A 118 58.20 -55.16 REMARK 500 LYS A 165 46.87 -103.25 REMARK 500 ARG A 167 -91.16 -157.01 REMARK 500 ASP A 172 12.23 -58.44 REMARK 500 GLU A 173 6.44 -160.93 REMARK 500 SER A 175 97.06 -42.53 REMARK 500 VAL A 193 -74.36 -62.87 REMARK 500 THR A 257 -71.70 -51.23 REMARK 500 TYR A 275 -128.74 31.44 REMARK 500 LYS A 297 -56.19 -18.82 REMARK 500 LYS A 337 64.15 -113.67 REMARK 500 LYS A 338 44.42 -100.36 REMARK 500 LEU A 339 -10.95 -144.52 REMARK 500 SER A 341 77.13 45.96 REMARK 500 LYS A 372 43.58 -92.41 REMARK 500 SER A 373 -76.44 165.21 REMARK 500 ASP A 380 -59.17 -26.38 REMARK 500 GLU A 417 167.39 172.46 REMARK 500 GLN A 422 65.16 -64.85 REMARK 500 SER A 429 66.63 -107.67 REMARK 500 TYR A 430 2.84 -160.42 REMARK 500 PHE A 431 119.45 -161.72 REMARK 500 ILE A 497 143.72 -39.60 REMARK 500 THR A 511 -55.06 -131.71 REMARK 500 ASN A 512 34.66 -140.21 REMARK 500 TYR A 525 -63.17 -128.22 REMARK 500 LEU A 553 -74.07 -108.48 REMARK 500 LYS A 561 -71.95 -96.67 REMARK 500 ASP A 562 103.40 -59.71 REMARK 500 GLU A 563 12.85 -69.38 REMARK 500 VAL A 564 -93.60 -100.90 REMARK 500 THR A 603 12.28 -68.49 REMARK 500 LYS A 609 -65.91 -13.64 REMARK 500 LYS A 646 -18.02 -150.45 REMARK 500 PRO A 660 33.83 -91.53 REMARK 500 LEU A 663 142.55 169.54 REMARK 500 ASN B 57 86.03 -162.25 REMARK 500 ASN B 60 83.49 -166.45 REMARK 500 ARG B 95 -39.77 -19.46 REMARK 500 GLN B 99 -24.68 68.20 REMARK 500 LYS B 135 -71.56 -47.28 REMARK 500 LEU B 194 64.15 -104.39 REMARK 500 ASP B 203 88.18 -61.99 REMARK 500 GLN B 215 62.75 -49.84 REMARK 500 REMARK 500 THIS ENTRY HAS 98 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 LEU A 174 SER A 175 147.60 REMARK 500 GLY A 251 ILE A 252 139.22 REMARK 500 ASP A 296 LYS A 297 144.95 REMARK 500 ASN A 371 LYS A 372 142.76 REMARK 500 TYR A 430 PHE A 431 147.03 REMARK 500 PRO A 657 VAL A 658 -146.16 REMARK 500 VAL A 658 PRO A 659 145.59 REMARK 500 PRO A 660 PRO A 661 147.02 REMARK 500 LYS B 218 LEU B 219 142.79 REMARK 500 ASP B 346 MET B 347 141.66 REMARK 500 LYS B 358 ASN B 359 -144.37 REMARK 500 ASN B 359 GLY B 360 138.93 REMARK 500 ARG B 428 SER B 429 -142.12 REMARK 500 SER B 429 TYR B 430 -133.42 REMARK 500 ASN B 560 LYS B 561 145.56 REMARK 500 LYS B 600 ASP B 601 -149.16 REMARK 500 VAL B 612 VAL B 613 -144.83 REMARK 500 VAL B 613 PRO B 614 148.00 REMARK 500 ALA B 640 PRO B 641 -131.26 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 CEF A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CEF B 701 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VSK RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN THE APO FORM. DBREF 3VSL A 46 691 UNP Q8NWC2 Q8NWC2_STAAW 46 691 DBREF 3VSL 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 HET CEF A 701 26 HET CEF B 701 26 HETNAM CEF CEFOTAXIME, C3' CLEAVED, OPEN, BOUND FORM FORMUL 3 CEF 2(C14 H15 N5 O5 S2) FORMUL 5 HOH *256(H2 O) HELIX 1 1 THR A 98 LYS A 111 1 14 HELIX 2 2 THR A 121 HIS A 133 1 13 HELIX 3 3 HIS A 133 ALA A 139 1 7 HELIX 4 4 MET A 141 MET A 147 1 7 HELIX 5 5 LYS A 154 LYS A 165 1 12 HELIX 6 6 ARG A 167 LEU A 171 5 5 HELIX 7 7 SER A 175 ASN A 189 1 15 HELIX 8 8 SER A 205 LYS A 218 1 14 HELIX 9 9 LEU A 238 GLY A 243 1 6 HELIX 10 10 PRO A 253 GLU A 255 5 3 HELIX 11 11 LEU A 256 LYS A 263 1 8 HELIX 12 12 SER A 274 TYR A 280 1 7 HELIX 13 13 TYR A 280 ARG A 285 1 6 HELIX 14 14 ASP A 321 LYS A 337 1 17 HELIX 15 15 ILE A 381 SER A 386 1 6 HELIX 16 16 VAL A 390 SER A 393 5 4 HELIX 17 17 VAL A 394 ASN A 405 1 12 HELIX 18 18 ASN A 440 SER A 448 1 9 HELIX 19 19 SER A 449 ALA A 461 1 13 HELIX 20 20 ILE A 475 VAL A 489 1 15 HELIX 21 21 ASN A 513 SER A 521 1 9 HELIX 22 22 THR A 529 ASN A 542 1 14 HELIX 23 23 THR A 582 MET A 595 1 14 HELIX 24 24 GLY A 604 LYS A 609 1 6 HELIX 25 25 GLY A 666 LYS A 678 1 13 HELIX 26 26 GLN B 99 LYS B 111 1 13 HELIX 27 27 THR B 121 HIS B 133 1 13 HELIX 28 28 HIS B 133 ALA B 139 1 7 HELIX 29 29 MET B 141 GLY B 151 1 11 HELIX 30 30 LYS B 154 ILE B 166 1 13 HELIX 31 31 ARG B 167 ASP B 172 1 6 HELIX 32 32 LYS B 177 ASN B 189 1 13 HELIX 33 33 GLU B 208 GLN B 214 1 7 HELIX 34 34 LEU B 238 GLY B 243 1 6 HELIX 35 35 PRO B 253 GLU B 255 5 3 HELIX 36 36 LEU B 256 SER B 262 1 7 HELIX 37 37 SER B 274 TYR B 280 1 7 HELIX 38 38 TYR B 280 ARG B 285 1 6 HELIX 39 39 ASP B 321 LYS B 338 1 18 HELIX 40 40 ILE B 381 SER B 386 1 6 HELIX 41 41 VAL B 390 SER B 393 5 4 HELIX 42 42 VAL B 394 ASN B 405 1 12 HELIX 43 43 ASN B 440 LEU B 445 1 6 HELIX 44 44 VAL B 451 ALA B 461 1 11 HELIX 45 45 ILE B 475 VAL B 489 1 15 HELIX 46 46 ASN B 513 ILE B 522 1 10 HELIX 47 47 THR B 529 ASN B 542 1 14 HELIX 48 48 THR B 582 MET B 595 1 14 HELIX 49 49 GLY B 604 LYS B 609 1 6 HELIX 50 50 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 LYS A 52 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 ASN A 308 N GLU A 290 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 ASP A 227 N LYS A 86 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 HIS A 556 -1 O LEU A 553 N LYS A 317 SHEET 6 C 6 LEU A 567 LYS A 570 -1 O LYS A 568 N ILE A 555 SHEET 1 D 5 ALA A 366 LYS A 368 0 SHEET 2 D 5 ASN A 349 GLN A 355 -1 N ALA A 350 O GLY A 367 SHEET 3 D 5 LEU A 647 GLN A 656 -1 O VAL A 652 N MET A 351 SHEET 4 D 5 ARG A 631 ALA A 640 -1 N TYR A 636 O ILE A 651 SHEET 5 D 5 ALA A 616 VAL A 624 -1 N GLY A 620 O THR A 635 SHEET 1 E 2 VAL A 415 ASP A 416 0 SHEET 2 E 2 VAL A 437 SER A 438 -1 O VAL A 437 N ASP A 416 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 ILE B 55 0 SHEET 2 G 4 ILE B 61 SER B 66 -1 O SER B 66 N HIS B 50 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 GLU B 202 0 SHEET 2 H 3 VAL B 79 TYR B 91 -1 N TYR B 91 O GLN B 197 SHEET 3 H 3 VAL B 222 LYS B 231 -1 O ASN B 223 N THR B 90 SHEET 1 I 6 GLN B 197 GLU B 202 0 SHEET 2 I 6 VAL B 79 TYR B 91 -1 N TYR B 91 O GLN B 197 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 TYR B 636 O ILE B 651 SHEET 6 J 6 ALA B 616 THR B 621 -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 LINK OG SER A 392 C8 CEF A 701 1555 1555 1.50 LINK OG SER B 392 C8 CEF B 701 1555 1555 1.50 CISPEP 1 ALA A 640 PRO A 641 0 -11.20 SITE 1 AC1 11 SER A 392 HIS A 447 SER A 448 ASN A 450 SITE 2 AC1 11 ILE A 522 GLN A 524 THR A 619 GLY A 620 SITE 3 AC1 11 THR A 621 GLU A 623 PRO A 660 SITE 1 AC2 13 GLY B 391 SER B 392 HIS B 447 SER B 448 SITE 2 AC2 13 ASN B 450 ILE B 522 GLN B 524 THR B 603 SITE 3 AC2 13 THR B 619 GLY B 620 THR B 621 GLU B 623 SITE 4 AC2 13 PRO B 659 CRYST1 143.031 143.031 189.610 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 0.006991 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006991 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005274 0.00000