HEADER HYDROLASE 10-JUL-20 6XQY TITLE CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF PBP2 S310A FROM NEISSERIA TITLE 2 GONORRHOEAE AT PH 9.5 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 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, TRANSFERASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR B.A.FENTON,P.ZHOU,C.DAVIES REVDAT 3 18-OCT-23 6XQY 1 REMARK REVDAT 2 02-FEB-22 6XQY 1 JRNL REVDAT 1 21-JUL-21 6XQY 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. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 46670 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2333 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 44.9200 - 4.8800 0.99 2683 141 0.1499 0.1617 REMARK 3 2 4.8800 - 3.8800 1.00 2635 139 0.1354 0.1602 REMARK 3 3 3.8800 - 3.3900 1.00 2631 138 0.1537 0.1833 REMARK 3 4 3.3900 - 3.0800 1.00 2644 140 0.1736 0.1974 REMARK 3 5 3.0800 - 2.8600 0.98 2573 135 0.1817 0.1851 REMARK 3 6 2.8600 - 2.6900 1.00 2616 138 0.1699 0.2408 REMARK 3 7 2.6900 - 2.5500 0.99 2618 138 0.1732 0.2055 REMARK 3 8 2.5500 - 2.4400 1.00 2621 138 0.1695 0.2097 REMARK 3 9 2.4400 - 2.3500 1.00 2598 137 0.1761 0.2689 REMARK 3 10 2.3500 - 2.2700 1.00 2622 138 0.1810 0.2232 REMARK 3 11 2.2700 - 2.2000 1.00 2628 138 0.1755 0.2230 REMARK 3 12 2.2000 - 2.1300 1.00 2581 136 0.1943 0.2303 REMARK 3 13 2.1300 - 2.0800 0.96 2518 133 0.1997 0.2438 REMARK 3 14 2.0800 - 2.0300 0.98 2568 135 0.2144 0.2579 REMARK 3 15 2.0300 - 1.9800 0.99 2600 135 0.2085 0.2810 REMARK 3 16 1.9800 - 1.9400 0.99 2583 136 0.2177 0.2840 REMARK 3 17 1.9400 - 1.9000 1.00 2618 138 0.2299 0.2828 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) : 0.197 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.432 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.32 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.00 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 : 0.007 5061 REMARK 3 ANGLE : 0.902 6874 REMARK 3 CHIRALITY : 0.056 769 REMARK 3 PLANARITY : 0.006 902 REMARK 3 DIHEDRAL : 23.709 1893 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 494 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.0245 -9.4217 8.1418 REMARK 3 T TENSOR REMARK 3 T11: 0.3456 T22: 0.2633 REMARK 3 T33: 0.2745 T12: -0.0302 REMARK 3 T13: -0.0066 T23: -0.0195 REMARK 3 L TENSOR REMARK 3 L11: 1.3720 L22: 1.8356 REMARK 3 L33: 1.8236 L12: -0.7944 REMARK 3 L13: -0.2275 L23: 0.1244 REMARK 3 S TENSOR REMARK 3 S11: 0.0414 S12: 0.1419 S13: -0.0672 REMARK 3 S21: -0.3415 S22: -0.0659 S23: -0.0251 REMARK 3 S31: 0.0653 S32: -0.0174 S33: 0.0001 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 495 THROUGH 573 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.7676 -11.9538 -3.9783 REMARK 3 T TENSOR REMARK 3 T11: 0.6364 T22: 0.3571 REMARK 3 T33: 0.3429 T12: 0.0506 REMARK 3 T13: 0.0128 T23: -0.0402 REMARK 3 L TENSOR REMARK 3 L11: 1.7046 L22: 0.8389 REMARK 3 L33: 0.4255 L12: -0.6192 REMARK 3 L13: -0.0642 L23: 0.3873 REMARK 3 S TENSOR REMARK 3 S11: 0.3535 S12: 0.3746 S13: -0.3179 REMARK 3 S21: -0.8711 S22: -0.4154 S23: -0.1617 REMARK 3 S31: 0.1742 S32: 0.0526 S33: -0.0476 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 236 THROUGH 281 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.6895 0.0334 50.7011 REMARK 3 T TENSOR REMARK 3 T11: 0.4331 T22: 0.4294 REMARK 3 T33: 0.3693 T12: -0.0433 REMARK 3 T13: 0.1032 T23: 0.0187 REMARK 3 L TENSOR REMARK 3 L11: 0.6345 L22: 0.8905 REMARK 3 L33: 1.3557 L12: 0.6546 REMARK 3 L13: 0.2300 L23: -0.1899 REMARK 3 S TENSOR REMARK 3 S11: 0.1168 S12: -0.4889 S13: -0.1969 REMARK 3 S21: 0.5122 S22: -0.0240 S23: 0.2439 REMARK 3 S31: 0.2531 S32: -0.2414 S33: 0.0003 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 282 THROUGH 405 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.0447 12.8836 30.0309 REMARK 3 T TENSOR REMARK 3 T11: 0.2182 T22: 0.3071 REMARK 3 T33: 0.3048 T12: 0.0189 REMARK 3 T13: -0.0052 T23: -0.0153 REMARK 3 L TENSOR REMARK 3 L11: 0.6107 L22: 1.4470 REMARK 3 L33: 1.5076 L12: -0.3688 REMARK 3 L13: -0.0464 L23: -0.1220 REMARK 3 S TENSOR REMARK 3 S11: -0.0233 S12: -0.0315 S13: 0.0666 REMARK 3 S21: -0.1189 S22: 0.0138 S23: 0.1503 REMARK 3 S31: -0.0681 S32: -0.2146 S33: 0.0000 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 406 THROUGH 494 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.0894 7.2972 35.9195 REMARK 3 T TENSOR REMARK 3 T11: 0.1653 T22: 0.2804 REMARK 3 T33: 0.2771 T12: 0.0073 REMARK 3 T13: -0.0176 T23: -0.0266 REMARK 3 L TENSOR REMARK 3 L11: 0.9672 L22: 1.7472 REMARK 3 L33: 1.7477 L12: -0.0168 REMARK 3 L13: -0.5081 L23: 0.4387 REMARK 3 S TENSOR REMARK 3 S11: -0.0302 S12: -0.1197 S13: 0.0691 REMARK 3 S21: 0.1068 S22: 0.0276 S23: -0.0323 REMARK 3 S31: 0.0008 S32: 0.0513 S33: 0.0000 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 495 THROUGH 522 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.4194 8.9477 36.2124 REMARK 3 T TENSOR REMARK 3 T11: 0.2033 T22: 0.4020 REMARK 3 T33: 0.4023 T12: 0.0126 REMARK 3 T13: 0.0471 T23: -0.0487 REMARK 3 L TENSOR REMARK 3 L11: 0.0328 L22: 0.2327 REMARK 3 L33: 0.3513 L12: 0.0234 REMARK 3 L13: -0.1028 L23: -0.0380 REMARK 3 S TENSOR REMARK 3 S11: -0.1070 S12: -0.0704 S13: -0.1078 REMARK 3 S21: 0.2249 S22: 0.0412 S23: 0.1730 REMARK 3 S31: -0.1373 S32: -0.1638 S33: -0.0540 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 523 THROUGH 544 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.8729 10.4289 46.1977 REMARK 3 T TENSOR REMARK 3 T11: 0.3367 T22: 0.3914 REMARK 3 T33: 0.5175 T12: 0.0399 REMARK 3 T13: 0.0629 T23: 0.0248 REMARK 3 L TENSOR REMARK 3 L11: 0.3122 L22: 0.5768 REMARK 3 L33: 0.6421 L12: 0.1814 REMARK 3 L13: -0.1002 L23: 0.4975 REMARK 3 S TENSOR REMARK 3 S11: -0.0135 S12: -0.0638 S13: 0.9424 REMARK 3 S21: 0.4636 S22: -0.0257 S23: 0.0758 REMARK 3 S31: -0.1498 S32: -0.1254 S33: -0.0072 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 545 THROUGH 574 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.2469 10.0979 55.5323 REMARK 3 T TENSOR REMARK 3 T11: 0.4944 T22: 0.4354 REMARK 3 T33: 0.3460 T12: -0.0181 REMARK 3 T13: 0.0002 T23: -0.0528 REMARK 3 L TENSOR REMARK 3 L11: 0.0635 L22: 0.3940 REMARK 3 L33: 0.2622 L12: 0.1812 REMARK 3 L13: 0.1358 L23: 0.3305 REMARK 3 S TENSOR REMARK 3 S11: 0.0557 S12: -0.1579 S13: 0.1334 REMARK 3 S21: 0.4481 S22: 0.0238 S23: -0.0104 REMARK 3 S31: -0.1585 S32: -0.0632 S33: 0.0002 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 236 THROUGH 241 OR REMARK 3 RESID 243 THROUGH 311 OR RESID 313 REMARK 3 THROUGH 344 OR RESID 346 THROUGH 355 OR REMARK 3 RESID 357 THROUGH 408 OR RESID 410 REMARK 3 THROUGH 471 OR RESID 473 THROUGH 489 OR REMARK 3 RESID 491 THROUGH 527 OR RESID 529 REMARK 3 THROUGH 543 OR RESID 545 THROUGH 566 OR REMARK 3 RESID 568 THROUGH 573)) REMARK 3 SELECTION : (CHAIN 'B' AND (RESID 236 THROUGH 241 OR REMARK 3 RESID 243 THROUGH 311 OR RESID 313 REMARK 3 THROUGH 344 OR RESID 346 THROUGH 355 OR REMARK 3 RESID 357 THROUGH 408 OR RESID 410 REMARK 3 THROUGH 471 OR RESID 473 THROUGH 489 OR REMARK 3 RESID 491 THROUGH 503 OR RESID 513 REMARK 3 THROUGH 527 OR RESID 529 THROUGH 543 OR REMARK 3 RESID 545 THROUGH 566 OR RESID 568 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 6XQY 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_1000250615. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-FEB-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 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 : 46696 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 44.920 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 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 (%): 42.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 13% PEG 400, 50 MM KCL, 12.5 MM TRIS, REMARK 280 12.5 MM BIS-TRIS, 25 MM SODIUM ACETATE (PH 9.5), VAPOR DIFFUSION, REMARK 280 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 38.27500 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 PHE A 504 REMARK 465 VAL A 505 REMARK 465 ASN A 506 REMARK 465 GLY A 507 REMARK 465 ARG A 508 REMARK 465 TYR A 509 REMARK 465 ALA A 510 REMARK 465 ASP A 511 REMARK 465 ASN A 512 REMARK 465 ALA A 574 REMARK 465 ASP B 235 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 HIS A 440 44.67 -92.86 REMARK 500 LEU A 447 156.18 78.37 REMARK 500 HIS B 440 45.93 -91.45 REMARK 500 LEU B 447 157.11 77.18 REMARK 500 ASN B 506 53.28 86.80 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 VAL B 505 ASN B 506 143.28 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 CL B 601 DBREF 6XQY A 237 282 UNP P08149 PBP2_NEIGO 237 282 DBREF 6XQY A 298 574 UNP P08149 PBP2_NEIGO 298 574 DBREF 6XQY B 237 282 UNP P08149 PBP2_NEIGO 237 282 DBREF 6XQY B 298 574 UNP P08149 PBP2_NEIGO 298 574 SEQADV 6XQY ASP A 235 UNP P08149 EXPRESSION TAG SEQADV 6XQY MET A 236 UNP P08149 EXPRESSION TAG SEQADV 6XQY GLY A 296 UNP P08149 LINKER SEQADV 6XQY GLY A 297 UNP P08149 LINKER SEQADV 6XQY ALA A 310 UNP P08149 SER 310 ENGINEERED MUTATION SEQADV 6XQY ASP B 235 UNP P08149 EXPRESSION TAG SEQADV 6XQY MET B 236 UNP P08149 EXPRESSION TAG SEQADV 6XQY GLY B 296 UNP P08149 LINKER SEQADV 6XQY GLY B 297 UNP P08149 LINKER SEQADV 6XQY ALA B 310 UNP P08149 SER 310 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 HIS 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 HIS 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 CL B 601 1 HETNAM CL CHLORIDE ION FORMUL 3 CL CL 1- FORMUL 4 HOH *142(H2 O) HELIX 1 AA1 ASP A 240 HIS A 258 1 19 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 VAL A 355 SER A 362 1 8 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 LEU A 428 HIS A 440 1 13 HELIX 11 AB2 LYS A 463 SER A 476 1 14 HELIX 12 AB3 GLY A 484 ALA A 488 5 5 HELIX 13 AB4 TYR A 544 ALA A 549 1 6 HELIX 14 AB5 ALA A 549 LEU A 564 1 16 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 ASN B 506 ALA B 510 5 5 HELIX 28 AD1 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 VAL A 265 O ALA A 279 SHEET 3 AA1 5 VAL A 529 ASP A 536 -1 O ILE A 530 N LEU A 268 SHEET 4 AA1 5 VAL A 515 ALA A 522 -1 N PHE A 518 O VAL A 533 SHEET 5 AA1 5 GLY A 495 ALA A 501 -1 N ALA A 501 O VAL A 515 SHEET 1 AA2 2 MET A 305 ILE A 306 0 SHEET 2 AA2 2 LEU A 426 SER A 427 -1 O LEU A 426 N ILE A 306 SHEET 1 AA3 2 ARG A 331 ASN A 333 0 SHEET 2 AA3 2 SER A 352 ASP A 354 -1 O LEU A 353 N LEU A 332 SHEET 1 AA4 2 TYR A 337 ILE A 339 0 SHEET 2 AA4 2 SER A 342 VAL A 344 -1 O VAL A 344 N TYR A 337 SHEET 1 AA5 2 VAL A 443 LEU A 444 0 SHEET 2 AA5 2 LYS A 459 ARG A 460 -1 O LYS A 459 N LEU A 444 SHEET 1 AA6 5 ILE B 275 THR B 281 0 SHEET 2 AA6 5 ALA B 262 ASP B 269 -1 N VAL B 265 O ALA B 279 SHEET 3 AA6 5 VAL B 529 ASP B 536 -1 O ALA B 532 N VAL B 266 SHEET 4 AA6 5 ASP B 511 ALA B 522 -1 N PHE B 518 O VAL B 533 SHEET 5 AA6 5 GLY B 495 VAL B 505 -1 N ALA B 501 O VAL B 515 SHEET 1 AA7 2 MET B 305 ILE B 306 0 SHEET 2 AA7 2 LEU B 426 SER B 427 -1 O LEU B 426 N ILE B 306 SHEET 1 AA8 2 ARG B 331 ASN B 333 0 SHEET 2 AA8 2 SER B 352 ASP B 354 -1 O LEU B 353 N LEU B 332 SHEET 1 AA9 2 TYR B 337 ILE B 339 0 SHEET 2 AA9 2 SER B 342 VAL B 344 -1 O VAL B 344 N TYR B 337 SHEET 1 AB1 2 VAL B 443 LEU B 444 0 SHEET 2 AB1 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 -4.42 CISPEP 2 ALA A 522 PRO A 523 0 -11.13 CISPEP 3 THR B 281 PRO B 282 0 -5.51 CISPEP 4 ALA B 522 PRO B 523 0 -10.80 SITE 1 AC1 1 ARG B 345 CRYST1 44.940 76.550 87.900 90.00 91.64 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 0.022252 0.000000 0.000636 0.00000 SCALE2 0.000000 0.013063 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011381 0.00000