HEADER HYDROLASE 10-JUL-20 6XQX TITLE CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF PBP2 S310A FROM NEISSERIA TITLE 2 GONORRHOEAE WITH THE H514A MUTATION AT PH 7.5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE PEPTIDOGLYCAN D,D-TRANSPEPTIDASE PENA; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PENICILLIN-BINDING PROTEIN 2,PBP-2; COMPND 5 EC: 3.4.16.4; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEISSERIA GONORRHOEAE; SOURCE 3 ORGANISM_TAXID: 485; SOURCE 4 GENE: PENA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PBP2, BETA-LACTAM, ANTIBIOTIC TARGET, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR B.A.FENTON,P.ZHOU,C.DAVIES REVDAT 3 18-OCT-23 6XQX 1 REMARK REVDAT 2 02-FEB-22 6XQX 1 JRNL REVDAT 1 21-JUL-21 6XQX 0 JRNL AUTH B.A.FENTON,J.TOMBERG,C.A.SCIANDRA,R.A.NICHOLAS,C.DAVIES, JRNL AUTH 2 P.ZHOU JRNL TITL MUTATIONS IN PBP2 FROM CEFTRIAXONE-RESISTANT NEISSERIA JRNL TITL 2 GONORRHOEAE ALTER THE DYNAMICS OF THE BETA 3-BETA 4 LOOP TO JRNL TITL 3 FAVOR A LOW-AFFINITY DRUG-BINDING STATE. JRNL REF J.BIOL.CHEM. V. 297 01188 2021 JRNL REFN ESSN 1083-351X JRNL PMID 34529975 JRNL DOI 10.1016/J.JBC.2021.101188 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.430 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 31203 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1559 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 44.5000 - 4.7800 0.91 2640 140 0.1635 0.1862 REMARK 3 2 4.7800 - 3.7900 0.94 2687 141 0.1783 0.1917 REMARK 3 3 3.7900 - 3.3200 0.90 2530 133 0.2243 0.2554 REMARK 3 4 3.3200 - 3.0100 0.95 2674 141 0.2545 0.2664 REMARK 3 5 3.0100 - 2.8000 0.97 2712 143 0.2552 0.3206 REMARK 3 6 2.8000 - 2.6300 0.97 2737 145 0.2709 0.2863 REMARK 3 7 2.6300 - 2.5000 0.98 2776 143 0.2566 0.3207 REMARK 3 8 2.5000 - 2.3900 0.98 2752 145 0.2673 0.2886 REMARK 3 9 2.3900 - 2.3000 0.95 2658 140 0.2731 0.3354 REMARK 3 10 2.3000 - 2.2200 0.98 2698 143 0.2712 0.3194 REMARK 3 11 2.2200 - 2.1500 0.98 2780 145 0.2925 0.3164 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.261 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.491 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 44.91 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.07 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.002 5077 REMARK 3 ANGLE : 0.614 6880 REMARK 3 CHIRALITY : 0.043 769 REMARK 3 PLANARITY : 0.004 898 REMARK 3 DIHEDRAL : 20.087 1879 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 236 THROUGH 308 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.2704 -23.6325 5.3727 REMARK 3 T TENSOR REMARK 3 T11: 0.9965 T22: 0.5441 REMARK 3 T33: 0.4003 T12: -0.1725 REMARK 3 T13: -0.1831 T23: 0.0606 REMARK 3 L TENSOR REMARK 3 L11: 1.1578 L22: 0.4653 REMARK 3 L33: 0.7050 L12: 0.6041 REMARK 3 L13: 0.0709 L23: -0.1655 REMARK 3 S TENSOR REMARK 3 S11: 0.3332 S12: -0.5396 S13: 0.0088 REMARK 3 S21: 1.3613 S22: -0.3606 S23: -0.2911 REMARK 3 S31: -0.5081 S32: -0.1050 S33: 0.0031 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 309 THROUGH 463 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.2115 -25.4741 -14.8196 REMARK 3 T TENSOR REMARK 3 T11: 0.4264 T22: 0.3326 REMARK 3 T33: 0.3195 T12: 0.0164 REMARK 3 T13: 0.0005 T23: -0.0046 REMARK 3 L TENSOR REMARK 3 L11: 0.9756 L22: 3.1496 REMARK 3 L33: 1.8494 L12: 1.0518 REMARK 3 L13: 0.1938 L23: 0.5035 REMARK 3 S TENSOR REMARK 3 S11: 0.0603 S12: 0.0040 S13: 0.0258 REMARK 3 S21: 0.3825 S22: -0.0286 S23: 0.1008 REMARK 3 S31: 0.0904 S32: 0.0230 S33: 0.0003 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 464 THROUGH 573 ) REMARK 3 ORIGIN FOR THE GROUP (A): -22.4424 -27.3724 1.5844 REMARK 3 T TENSOR REMARK 3 T11: 0.8703 T22: 0.4029 REMARK 3 T33: 0.4447 T12: -0.0914 REMARK 3 T13: 0.1237 T23: -0.0053 REMARK 3 L TENSOR REMARK 3 L11: 1.6318 L22: 1.7474 REMARK 3 L33: 1.2022 L12: 1.4001 REMARK 3 L13: 0.2082 L23: -0.5719 REMARK 3 S TENSOR REMARK 3 S11: 0.3365 S12: -0.2434 S13: -0.1675 REMARK 3 S21: 1.1201 S22: -0.3341 S23: 0.3005 REMARK 3 S31: -0.1190 S32: -0.0206 S33: 0.0038 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 237 THROUGH 281 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.3056 -14.5272 -50.4799 REMARK 3 T TENSOR REMARK 3 T11: 0.6734 T22: 0.6448 REMARK 3 T33: 0.4379 T12: 0.0661 REMARK 3 T13: 0.1357 T23: 0.0827 REMARK 3 L TENSOR REMARK 3 L11: 0.5643 L22: 0.6311 REMARK 3 L33: 0.8551 L12: -0.5488 REMARK 3 L13: -0.1490 L23: 0.4318 REMARK 3 S TENSOR REMARK 3 S11: 0.2002 S12: 0.0326 S13: -0.0728 REMARK 3 S21: -0.5979 S22: -0.2819 S23: -0.2310 REMARK 3 S31: 0.1272 S32: 0.2427 S33: -0.0004 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 282 THROUGH 439 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.1285 -3.8391 -29.0809 REMARK 3 T TENSOR REMARK 3 T11: 0.3221 T22: 0.4532 REMARK 3 T33: 0.3977 T12: -0.0720 REMARK 3 T13: -0.0176 T23: -0.0140 REMARK 3 L TENSOR REMARK 3 L11: 1.5521 L22: 1.8458 REMARK 3 L33: 2.3999 L12: 0.8808 REMARK 3 L13: -0.3820 L23: -0.7063 REMARK 3 S TENSOR REMARK 3 S11: 0.0687 S12: -0.1108 S13: 0.1321 REMARK 3 S21: 0.0672 S22: -0.0171 S23: -0.1309 REMARK 3 S31: -0.1881 S32: 0.3678 S33: -0.0001 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 440 THROUGH 463 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.9878 -19.2327 -38.2443 REMARK 3 T TENSOR REMARK 3 T11: 0.5639 T22: 0.4958 REMARK 3 T33: 0.3334 T12: -0.0651 REMARK 3 T13: -0.0140 T23: -0.0415 REMARK 3 L TENSOR REMARK 3 L11: 0.4794 L22: 0.2368 REMARK 3 L33: 0.2646 L12: 0.2000 REMARK 3 L13: 0.0246 L23: -0.1925 REMARK 3 S TENSOR REMARK 3 S11: 0.0656 S12: 0.7406 S13: -0.0117 REMARK 3 S21: -0.3236 S22: -0.1298 S23: 0.0108 REMARK 3 S31: 0.5755 S32: -0.6336 S33: 0.0008 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 464 THROUGH 536 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.5526 -3.8955 -41.7030 REMARK 3 T TENSOR REMARK 3 T11: 0.3818 T22: 0.4542 REMARK 3 T33: 0.3921 T12: -0.0240 REMARK 3 T13: 0.0317 T23: 0.0925 REMARK 3 L TENSOR REMARK 3 L11: 0.7299 L22: 2.2445 REMARK 3 L33: 1.3408 L12: 0.2202 REMARK 3 L13: -0.5784 L23: 0.1333 REMARK 3 S TENSOR REMARK 3 S11: 0.0493 S12: 0.2493 S13: 0.2878 REMARK 3 S21: -0.3633 S22: -0.0285 S23: -0.0741 REMARK 3 S31: -0.0105 S32: 0.1842 S33: -0.0008 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 537 THROUGH 574 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.9192 -3.4395 -52.6809 REMARK 3 T TENSOR REMARK 3 T11: 0.5584 T22: 0.6141 REMARK 3 T33: 0.5524 T12: -0.0241 REMARK 3 T13: 0.0668 T23: 0.0698 REMARK 3 L TENSOR REMARK 3 L11: 0.3089 L22: 0.9435 REMARK 3 L33: 0.3383 L12: -0.2808 REMARK 3 L13: -0.1327 L23: -0.3291 REMARK 3 S TENSOR REMARK 3 S11: 0.1375 S12: -0.0933 S13: 0.5441 REMARK 3 S21: -0.4884 S22: -0.0895 S23: -0.2078 REMARK 3 S31: -0.1554 S32: 0.0917 S33: 0.0000 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: (CHAIN 'A' AND (RESID 237 THROUGH 304 OR REMARK 3 RESID 306 THROUGH 344 OR RESID 346 REMARK 3 THROUGH 361 OR RESID 363 THROUGH 383 OR REMARK 3 RESID 385 THROUGH 454 OR (RESID 455 AND REMARK 3 (NAME N OR NAME CA OR NAME C OR NAME O )) REMARK 3 OR RESID 456 THROUGH 489 OR RESID 491 REMARK 3 THROUGH 503 OR RESID 505 THROUGH 573)) REMARK 3 SELECTION : (CHAIN 'B' AND (RESID 237 THROUGH 304 OR REMARK 3 RESID 306 THROUGH 344 OR RESID 346 REMARK 3 THROUGH 361 OR RESID 363 THROUGH 383 OR REMARK 3 RESID 385 THROUGH 489 OR RESID 491 REMARK 3 THROUGH 503 OR RESID 505 OR RESID 509 REMARK 3 THROUGH 573)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6XQX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1000250614. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-OCT-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31251 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 44.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.0700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.160 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 1.17.1_3660 REMARK 200 STARTING MODEL: 6P53 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 1500, 0.062 M TRIS PH 7.5, 50 REMARK 280 MM KCL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 38.65500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 ASP A 235 REMARK 465 ASN A 506 REMARK 465 GLY A 507 REMARK 465 ARG A 508 REMARK 465 ALA A 574 REMARK 465 ASP B 235 REMARK 465 MET B 236 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ALA B 455 CB 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 PRO A 282 34.57 -74.63 REMARK 500 SER A 362 72.77 57.53 REMARK 500 HIS A 440 39.54 -88.78 REMARK 500 LEU A 447 151.17 76.11 REMARK 500 HIS B 440 41.21 -88.39 REMARK 500 LEU B 447 152.57 76.17 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 EDO A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 604 DBREF 6XQX A 237 282 UNP P08149 PBP2_NEIGO 237 282 DBREF 6XQX A 298 574 UNP P08149 PBP2_NEIGO 298 574 DBREF 6XQX B 237 282 UNP P08149 PBP2_NEIGO 237 282 DBREF 6XQX B 298 574 UNP P08149 PBP2_NEIGO 298 574 SEQADV 6XQX ASP A 235 UNP P08149 EXPRESSION TAG SEQADV 6XQX MET A 236 UNP P08149 EXPRESSION TAG SEQADV 6XQX GLY A 296 UNP P08149 LINKER SEQADV 6XQX GLY A 297 UNP P08149 LINKER SEQADV 6XQX ALA A 310 UNP P08149 SER 310 ENGINEERED MUTATION SEQADV 6XQX ALA A 514 UNP P08149 HIS 514 ENGINEERED MUTATION SEQADV 6XQX ASP B 235 UNP P08149 EXPRESSION TAG SEQADV 6XQX MET B 236 UNP P08149 EXPRESSION TAG SEQADV 6XQX GLY B 296 UNP P08149 LINKER SEQADV 6XQX GLY B 297 UNP P08149 LINKER SEQADV 6XQX ALA B 310 UNP P08149 SER 310 ENGINEERED MUTATION SEQADV 6XQX ALA B 514 UNP P08149 HIS 514 ENGINEERED MUTATION SEQRES 1 A 327 ASP MET LEU SER LEU ASP GLN ARG ILE GLN THR LEU ALA SEQRES 2 A 327 TYR GLU GLU LEU ASN LYS ALA VAL GLU TYR HIS GLN ALA SEQRES 3 A 327 LYS ALA GLY THR VAL VAL VAL LEU ASP ALA ARG THR GLY SEQRES 4 A 327 GLU ILE LEU ALA LEU ALA ASN THR PRO GLY GLY ARG ASN SEQRES 5 A 327 ARG ALA VAL THR ASP MET ILE GLU PRO GLY ALA ALA ILE SEQRES 6 A 327 LYS PRO PHE VAL ILE ALA LYS ALA LEU ASP ALA GLY LYS SEQRES 7 A 327 THR ASP LEU ASN GLU ARG LEU ASN THR GLN PRO TYR LYS SEQRES 8 A 327 ILE GLY PRO SER PRO VAL ARG ASP THR HIS VAL TYR PRO SEQRES 9 A 327 SER LEU ASP VAL ARG GLY ILE MET GLN LYS SER SER ASN SEQRES 10 A 327 VAL GLY THR SER LYS LEU SER ALA ARG PHE GLY ALA GLU SEQRES 11 A 327 GLU MET TYR ASP PHE TYR HIS GLU LEU GLY ILE GLY VAL SEQRES 12 A 327 ARG MET HIS SER GLY PHE PRO GLY GLU THR ALA GLY LEU SEQRES 13 A 327 LEU ARG ASN TRP ARG ARG TRP ARG PRO ILE GLU GLN ALA SEQRES 14 A 327 THR MET SER PHE GLY TYR GLY LEU GLN LEU SER LEU LEU SEQRES 15 A 327 GLN LEU ALA ARG ALA TYR THR ALA LEU THR HIS ASP GLY SEQRES 16 A 327 VAL LEU LEU PRO LEU SER PHE GLU LYS GLN ALA VAL ALA SEQRES 17 A 327 PRO GLN GLY LYS ARG ILE PHE LYS GLU SER THR ALA ARG SEQRES 18 A 327 GLU VAL ARG ASN LEU MET VAL SER VAL THR GLU PRO GLY SEQRES 19 A 327 GLY THR GLY THR ALA GLY ALA VAL ASP GLY PHE ASP VAL SEQRES 20 A 327 GLY ALA LYS THR GLY THR ALA ARG LYS PHE VAL ASN GLY SEQRES 21 A 327 ARG TYR ALA ASP ASN LYS ALA VAL ALA THR PHE ILE GLY SEQRES 22 A 327 PHE ALA PRO ALA LYS ASN PRO ARG VAL ILE VAL ALA VAL SEQRES 23 A 327 THR ILE ASP GLU PRO THR ALA HIS GLY TYR TYR GLY GLY SEQRES 24 A 327 VAL VAL ALA GLY PRO PRO PHE LYS LYS ILE MET GLY GLY SEQRES 25 A 327 SER LEU ASN ILE LEU GLY ILE SER PRO THR LYS PRO LEU SEQRES 26 A 327 THR ALA SEQRES 1 B 327 ASP MET LEU SER LEU ASP GLN ARG ILE GLN THR LEU ALA SEQRES 2 B 327 TYR GLU GLU LEU ASN LYS ALA VAL GLU TYR HIS GLN ALA SEQRES 3 B 327 LYS ALA GLY THR VAL VAL VAL LEU ASP ALA ARG THR GLY SEQRES 4 B 327 GLU ILE LEU ALA LEU ALA ASN THR PRO GLY GLY ARG ASN SEQRES 5 B 327 ARG ALA VAL THR ASP MET ILE GLU PRO GLY ALA ALA ILE SEQRES 6 B 327 LYS PRO PHE VAL ILE ALA LYS ALA LEU ASP ALA GLY LYS SEQRES 7 B 327 THR ASP LEU ASN GLU ARG LEU ASN THR GLN PRO TYR LYS SEQRES 8 B 327 ILE GLY PRO SER PRO VAL ARG ASP THR HIS VAL TYR PRO SEQRES 9 B 327 SER LEU ASP VAL ARG GLY ILE MET GLN LYS SER SER ASN SEQRES 10 B 327 VAL GLY THR SER LYS LEU SER ALA ARG PHE GLY ALA GLU SEQRES 11 B 327 GLU MET TYR ASP PHE TYR HIS GLU LEU GLY ILE GLY VAL SEQRES 12 B 327 ARG MET HIS SER GLY PHE PRO GLY GLU THR ALA GLY LEU SEQRES 13 B 327 LEU ARG ASN TRP ARG ARG TRP ARG PRO ILE GLU GLN ALA SEQRES 14 B 327 THR MET SER PHE GLY TYR GLY LEU GLN LEU SER LEU LEU SEQRES 15 B 327 GLN LEU ALA ARG ALA TYR THR ALA LEU THR HIS ASP GLY SEQRES 16 B 327 VAL LEU LEU PRO LEU SER PHE GLU LYS GLN ALA VAL ALA SEQRES 17 B 327 PRO GLN GLY LYS ARG ILE PHE LYS GLU SER THR ALA ARG SEQRES 18 B 327 GLU VAL ARG ASN LEU MET VAL SER VAL THR GLU PRO GLY SEQRES 19 B 327 GLY THR GLY THR ALA GLY ALA VAL ASP GLY PHE ASP VAL SEQRES 20 B 327 GLY ALA LYS THR GLY THR ALA ARG LYS PHE VAL ASN GLY SEQRES 21 B 327 ARG TYR ALA ASP ASN LYS ALA VAL ALA THR PHE ILE GLY SEQRES 22 B 327 PHE ALA PRO ALA LYS ASN PRO ARG VAL ILE VAL ALA VAL SEQRES 23 B 327 THR ILE ASP GLU PRO THR ALA HIS GLY TYR TYR GLY GLY SEQRES 24 B 327 VAL VAL ALA GLY PRO PRO PHE LYS LYS ILE MET GLY GLY SEQRES 25 B 327 SER LEU ASN ILE LEU GLY ILE SER PRO THR LYS PRO LEU SEQRES 26 B 327 THR ALA HET EDO A 601 4 HET SO4 A 602 5 HET EDO B 601 4 HET EDO B 602 4 HET EDO B 603 4 HET EDO B 604 4 HETNAM EDO 1,2-ETHANEDIOL HETNAM SO4 SULFATE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 3 EDO 5(C2 H6 O2) FORMUL 4 SO4 O4 S 2- FORMUL 9 HOH *70(H2 O) HELIX 1 AA1 ASP A 240 GLN A 259 1 20 HELIX 2 AA2 ASN A 299 ASP A 304 1 6 HELIX 3 AA3 PRO A 308 ALA A 311 5 4 HELIX 4 AA4 ILE A 312 ALA A 323 1 12 HELIX 5 AA5 ASP A 354 SER A 362 1 9 HELIX 6 AA6 SER A 363 ALA A 372 1 10 HELIX 7 AA7 GLY A 375 LEU A 386 1 12 HELIX 8 AA8 ASN A 406 TRP A 410 5 5 HELIX 9 AA9 ARG A 411 PHE A 420 1 10 HELIX 10 AB1 SER A 427 TYR A 435 1 9 HELIX 11 AB2 TYR A 435 HIS A 440 1 6 HELIX 12 AB3 LYS A 463 SER A 476 1 14 HELIX 13 AB4 GLY A 484 ALA A 488 5 5 HELIX 14 AB5 TYR A 544 LEU A 564 1 21 HELIX 15 AB6 ASP B 240 HIS B 258 1 19 HELIX 16 AB7 ASN B 299 ASP B 304 1 6 HELIX 17 AB8 PRO B 308 ALA B 311 5 4 HELIX 18 AB9 ILE B 312 ALA B 323 1 12 HELIX 19 AC1 VAL B 355 SER B 362 1 8 HELIX 20 AC2 SER B 363 ALA B 372 1 10 HELIX 21 AC3 GLY B 375 LEU B 386 1 12 HELIX 22 AC4 ASN B 406 TRP B 410 5 5 HELIX 23 AC5 ARG B 411 PHE B 420 1 10 HELIX 24 AC6 LEU B 428 HIS B 440 1 13 HELIX 25 AC7 LYS B 463 SER B 476 1 14 HELIX 26 AC8 GLY B 484 ALA B 488 5 5 HELIX 27 AC9 TYR B 544 LEU B 564 1 21 SHEET 1 AA1 5 ILE A 275 THR A 281 0 SHEET 2 AA1 5 ALA A 262 ASP A 269 -1 N GLY A 263 O THR A 281 SHEET 3 AA1 5 VAL A 529 ASP A 536 -1 O ALA A 532 N VAL A 266 SHEET 4 AA1 5 ALA A 514 ALA A 522 -1 N ALA A 516 O ILE A 535 SHEET 5 AA1 5 GLY A 495 ARG A 502 -1 N LYS A 497 O ILE A 519 SHEET 1 AA2 2 LEU A 332 ASN A 333 0 SHEET 2 AA2 2 SER A 352 LEU A 353 -1 O LEU A 353 N LEU A 332 SHEET 1 AA3 2 TYR A 337 ILE A 339 0 SHEET 2 AA3 2 SER A 342 VAL A 344 -1 O VAL A 344 N TYR A 337 SHEET 1 AA4 2 VAL A 443 LEU A 444 0 SHEET 2 AA4 2 LYS A 459 ARG A 460 -1 O LYS A 459 N LEU A 444 SHEET 1 AA5 7 ILE B 275 THR B 281 0 SHEET 2 AA5 7 ALA B 262 ASP B 269 -1 N GLY B 263 O THR B 281 SHEET 3 AA5 7 VAL B 529 ASP B 536 -1 O THR B 534 N THR B 264 SHEET 4 AA5 7 ASP B 511 ALA B 522 -1 N ALA B 516 O ILE B 535 SHEET 5 AA5 7 GLY B 495 VAL B 505 -1 N ALA B 501 O VAL B 515 SHEET 6 AA5 7 MET B 305 GLU B 307 -1 N GLU B 307 O ARG B 502 SHEET 7 AA5 7 LEU B 426 SER B 427 -1 O LEU B 426 N ILE B 306 SHEET 1 AA6 2 ARG B 331 ASN B 333 0 SHEET 2 AA6 2 SER B 352 ASP B 354 -1 O LEU B 353 N LEU B 332 SHEET 1 AA7 2 TYR B 337 ILE B 339 0 SHEET 2 AA7 2 SER B 342 VAL B 344 -1 O VAL B 344 N TYR B 337 SHEET 1 AA8 2 VAL B 443 LEU B 444 0 SHEET 2 AA8 2 LYS B 459 ARG B 460 -1 O LYS B 459 N LEU B 444 CISPEP 1 THR A 281 PRO A 282 0 -2.12 CISPEP 2 ALA A 522 PRO A 523 0 -7.86 CISPEP 3 THR B 281 PRO B 282 0 -6.03 CISPEP 4 ALA B 522 PRO B 523 0 -8.09 SITE 1 AC1 5 GLU A 385 LYS B 319 ARG B 508 TYR B 509 SITE 2 AC1 5 EDO B 603 SITE 1 AC2 4 THR A 498 GLY A 499 THR A 500 HOH A 727 SITE 1 AC3 4 LYS B 261 ASP B 441 ARG B 468 ARG B 471 SITE 1 AC4 9 ASP B 322 ARG B 460 ILE B 461 PHE B 462 SITE 2 AC4 9 LYS B 463 GLY B 507 TYR B 509 EDO B 603 SITE 3 AC4 9 HOH B 711 SITE 1 AC5 6 EDO A 601 GLU B 385 ARG B 460 ILE B 461 SITE 2 AC5 6 ARG B 508 EDO B 602 SITE 1 AC6 2 ARG B 408 TRP B 410 CRYST1 44.520 77.310 88.180 90.00 91.62 90.00 P 1 21 1 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 0.022462 0.000000 0.000636 0.00000 SCALE2 0.000000 0.012935 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011345 0.00000