HEADER TRANSFERASE/TRANSFERASE INHIBITOR 30-JAN-19 6NTW TITLE CRYSTAL STRUCTURE OF E. COLI YCBB COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE L,D-TRANSPEPTIDASE YCBB; COMPND 3 CHAIN: A; COMPND 4 EC: 2.-.-.-; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: MEROPENEM-ACYLATED YCBB SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI (STRAIN K12); SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: YCBB, B0925, JW0908; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS L, D-TRANSPEPTIDASE, TRANSFERASE, TRANSFERASE-TRANSFERASE INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.A.CAVENEY,N.C.J.STRYNADKA,G.CABALLERO,L.J.WORRALL REVDAT 3 08-JAN-20 6NTW 1 REMARK REVDAT 2 08-MAY-19 6NTW 1 JRNL REVDAT 1 20-MAR-19 6NTW 0 JRNL AUTH N.A.CAVENEY,G.CABALLERO,H.VOEDTS,A.NICIFOROVIC,L.J.WORRALL, JRNL AUTH 2 M.VUCKOVIC,M.FONVIELLE,J.E.HUGONNET,M.ARTHUR,N.C.J.STRYNADKA JRNL TITL STRUCTURAL INSIGHT INTO YCBB-MEDIATED BETA-LACTAM RESISTANCE JRNL TITL 2 IN ESCHERICHIA COLI. JRNL REF NAT COMMUN V. 10 1849 2019 JRNL REFN ESSN 2041-1723 JRNL PMID 31015395 JRNL DOI 10.1038/S41467-019-09507-0 REMARK 2 REMARK 2 RESOLUTION. 2.76 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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) : 2.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 89.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 18943 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.258 REMARK 3 R VALUE (WORKING SET) : 0.256 REMARK 3 FREE R VALUE : 0.298 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 953 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 89.4953 - 5.2794 1.00 2736 158 0.2130 0.2389 REMARK 3 2 5.2794 - 4.1904 1.00 2617 127 0.2163 0.2465 REMARK 3 3 4.1904 - 3.6607 1.00 2593 127 0.2434 0.2872 REMARK 3 4 3.6607 - 3.3260 1.00 2544 138 0.2821 0.3767 REMARK 3 5 3.3260 - 3.0876 0.99 2519 142 0.3226 0.3833 REMARK 3 6 3.0876 - 2.9056 0.98 2512 129 0.3775 0.4405 REMARK 3 7 2.9056 - 2.7600 0.98 2469 132 0.4179 0.4302 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) : 0.470 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.700 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 65.64 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.013 4143 REMARK 3 ANGLE : 1.878 5654 REMARK 3 CHIRALITY : 0.110 618 REMARK 3 PLANARITY : 0.014 737 REMARK 3 DIHEDRAL : 19.059 1543 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 6NTW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-JAN-19. REMARK 100 THE DEPOSITION ID IS D_1000239421. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAR-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 : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9774 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.6.2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18943 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 89.448 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.4 REMARK 200 DATA REDUNDANCY : 9.400 REMARK 200 R MERGE (I) : 0.41500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 33.6 REMARK 200 DATA REDUNDANCY IN SHELL : 1.40 REMARK 200 R MERGE FOR SHELL (I) : 0.04300 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 UL PROTEIN SOLUTION (30 MG/ML REMARK 280 PURIFIED PROTEIN IN 20 MM HEPES PH 8.0, 300 MM NACL) AND 1 UL OF REMARK 280 MOTHER LIQUOR (1.44 M LITHIUM SULFATE, 0.08 M HEPES PH 7.5, 0.02 REMARK 280 M SODIUM ACETATE PH 4.6, 0.015 M AMMONIUM SULFATE, 4% (W/V) REMARK 280 POLYETHYLENE GLYCOL (PEG) 2000 MONOMETHYL ETHER (MME)) WITH THE REMARK 280 ADDITION OF 1 MM MEROPENEM AND L-ALA-D-GLU-MDAP-D-ALA AT 1 MM, REMARK 280 VAPOR DIFFUSION, TEMPERATURE 298.15K 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 44.40050 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 63.24950 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 63.24950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 66.60075 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 63.24950 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 63.24950 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 22.20025 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 63.24950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 63.24950 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 66.60075 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 63.24950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 63.24950 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 22.20025 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 44.40050 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: 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 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 31 REMARK 465 GLU A 32 REMARK 465 PRO A 33 REMARK 465 GLU A 34 REMARK 465 VAL A 35 REMARK 465 ILE A 36 REMARK 465 ALA A 54 REMARK 465 GLN A 55 REMARK 465 ALA A 56 REMARK 465 THR A 57 REMARK 465 ALA A 58 REMARK 465 ILE A 59 REMARK 465 MET A 60 REMARK 465 ALA A 61 REMARK 465 GLY A 62 REMARK 465 ILE A 63 REMARK 465 GLN A 64 REMARK 465 PRO A 65 REMARK 465 LEU A 66 REMARK 465 PRO A 67 REMARK 465 GLU A 68 REMARK 465 GLY A 69 REMARK 465 ALA A 70 REMARK 465 ALA A 71 REMARK 465 GLU A 72 REMARK 465 LYS A 73 REMARK 465 GLY A 267 REMARK 465 GLY A 268 REMARK 465 PRO A 269 REMARK 465 LYS A 270 REMARK 465 ILE A 271 REMARK 465 THR A 272 REMARK 465 LEU A 273 REMARK 465 PRO A 274 REMARK 465 GLY A 275 REMARK 465 ASP A 276 REMARK 465 ASP A 277 REMARK 465 THR A 278 REMARK 465 PRO A 279 REMARK 465 THR A 280 REMARK 465 ASP A 281 REMARK 465 ALA A 282 REMARK 465 VAL A 283 REMARK 465 VAL A 284 REMARK 465 SER A 285 REMARK 465 PRO A 286 REMARK 465 SER A 287 REMARK 465 ALA A 288 REMARK 465 VAL A 289 REMARK 465 THR A 290 REMARK 465 VAL A 291 REMARK 465 GLU A 292 REMARK 465 THR A 293 REMARK 465 ALA A 294 REMARK 465 GLU A 295 REMARK 465 THR A 296 REMARK 465 LYS A 297 REMARK 465 PRO A 298 REMARK 465 MET A 299 REMARK 465 ASP A 300 REMARK 465 LYS A 301 REMARK 465 GLN A 302 REMARK 465 THR A 303 REMARK 465 THR A 304 REMARK 465 SER A 305 REMARK 465 ARG A 306 REMARK 465 SER A 307 REMARK 465 LYS A 308 REMARK 465 PRO A 309 REMARK 465 ALA A 310 REMARK 465 PRO A 311 REMARK 465 ALA A 312 REMARK 465 VAL A 313 REMARK 465 ARG A 314 REMARK 465 ASN A 459 REMARK 465 ALA A 600 REMARK 465 ARG A 601 REMARK 465 SER A 602 REMARK 465 SER A 603 REMARK 465 SER A 604 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 LYS A 609 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE1 GLN A 485 O ASN A 491 1.47 REMARK 500 SG CYS A 528 O6 MXR A 701 1.65 REMARK 500 O GLN A 247 O ALA A 316 1.85 REMARK 500 NH1 ARG A 173 O3 SO4 A 703 1.89 REMARK 500 O ASN A 422 OG1 THR A 561 1.92 REMARK 500 OH TYR A 317 O GLY A 338 2.05 REMARK 500 O HIS A 214 O HOH A 801 2.09 REMARK 500 OG SER A 374 N GLY A 392 2.10 REMARK 500 NH1 ARG A 173 O2 SO4 A 703 2.13 REMARK 500 O ARG A 345 ND2 ASN A 349 2.13 REMARK 500 NH1 ARG A 173 S SO4 A 703 2.16 REMARK 500 SG CYS A 528 C3 MXR A 701 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 CZ ARG A 456 CZ ARG A 456 8556 0.64 REMARK 500 CZ ARG A 456 NH1 ARG A 456 8556 0.69 REMARK 500 NE ARG A 456 NH1 ARG A 456 8556 0.96 REMARK 500 NH1 ARG A 456 NH2 ARG A 456 8556 1.34 REMARK 500 CD ARG A 456 CD ARG A 456 8556 1.58 REMARK 500 CZ ARG A 456 NH2 ARG A 456 8556 1.68 REMARK 500 NH2 ARG A 456 NH2 ARG A 456 8556 1.72 REMARK 500 NE ARG A 456 CZ ARG A 456 8556 1.79 REMARK 500 NH1 ARG A 456 NH1 ARG A 456 8556 1.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU A 120 CB - CG - CD2 ANGL. DEV. = -10.5 DEGREES REMARK 500 LEU A 138 CA - CB - CG ANGL. DEV. = 16.1 DEGREES REMARK 500 ARG A 173 NE - CZ - NH1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ARG A 173 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 TYR A 446 C - N - CA ANGL. DEV. = 27.3 DEGREES REMARK 500 ARG A 482 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 TYR A 507 CB - CG - CD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 CYS A 528 N - CA - CB ANGL. DEV. = 9.9 DEGREES REMARK 500 TYR A 575 CB - CG - CD2 ANGL. DEV. = -4.8 DEGREES REMARK 500 TYR A 576 CA - CB - CG ANGL. DEV. = 14.8 DEGREES REMARK 500 TYR A 576 CB - CG - CD2 ANGL. DEV. = -8.5 DEGREES REMARK 500 TYR A 576 CB - CG - CD1 ANGL. DEV. = 4.2 DEGREES REMARK 500 TYR A 589 CB - CG - CD2 ANGL. DEV. = -3.8 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 LEU A 51 132.63 -177.83 REMARK 500 MET A 103 -1.27 67.74 REMARK 500 ASN A 145 -62.01 -129.00 REMARK 500 LYS A 240 -7.41 59.00 REMARK 500 ALA A 316 -24.18 -147.53 REMARK 500 TYR A 317 71.12 59.56 REMARK 500 THR A 375 74.97 59.39 REMARK 500 SER A 492 0.20 86.01 REMARK 500 ALA A 545 -167.35 -100.75 REMARK 500 LEU A 598 139.95 -176.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 176 0.05 SIDE CHAIN REMARK 500 TYR A 507 0.08 SIDE CHAIN REMARK 500 TYR A 575 0.08 SIDE CHAIN REMARK 500 TYR A 576 0.08 SIDE CHAIN REMARK 500 TYR A 589 0.06 SIDE CHAIN 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 MXR A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 705 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 706 DBREF 6NTW A 31 615 UNP P22525 YCBB_ECOLI 31 615 SEQRES 1 A 585 ASP GLU PRO GLU VAL ILE PRO GLY ASP SER PRO VAL ALA SEQRES 2 A 585 VAL SER GLU GLN GLY GLU ALA LEU PRO GLN ALA GLN ALA SEQRES 3 A 585 THR ALA ILE MET ALA GLY ILE GLN PRO LEU PRO GLU GLY SEQRES 4 A 585 ALA ALA GLU LYS ALA ARG THR GLN ILE GLU SER GLN LEU SEQRES 5 A 585 PRO ALA GLY TYR LYS PRO VAL TYR LEU ASN GLN LEU GLN SEQRES 6 A 585 LEU LEU TYR ALA ALA ARG ASP MET GLN PRO MET TRP GLU SEQRES 7 A 585 ASN ARG ASP ALA VAL LYS ALA PHE GLN GLN GLN LEU ALA SEQRES 8 A 585 GLU VAL ALA ILE ALA GLY PHE GLN PRO GLN PHE ASN LYS SEQRES 9 A 585 TRP VAL GLU LEU LEU THR ASP PRO GLY VAL ASN GLY MET SEQRES 10 A 585 ALA ARG ASP VAL VAL LEU SER ASP ALA MET MET GLY TYR SEQRES 11 A 585 LEU HIS PHE ILE ALA ASN ILE PRO VAL LYS GLY THR ARG SEQRES 12 A 585 TRP LEU TYR SER SER LYS PRO TYR ALA LEU ALA THR PRO SEQRES 13 A 585 PRO LEU SER VAL ILE ASN GLN TRP GLN LEU ALA LEU ASP SEQRES 14 A 585 LYS GLY GLN LEU PRO THR PHE VAL ALA GLY LEU ALA PRO SEQRES 15 A 585 GLN HIS PRO GLN TYR ALA ALA MET HIS GLU SER LEU LEU SEQRES 16 A 585 ALA LEU LEU CYS ASP THR LYS PRO TRP PRO GLN LEU THR SEQRES 17 A 585 GLY LYS ALA THR LEU ARG PRO GLY GLN TRP SER ASN ASP SEQRES 18 A 585 VAL PRO ALA LEU ARG GLU ILE LEU GLN ARG THR GLY MET SEQRES 19 A 585 LEU ASP GLY GLY PRO LYS ILE THR LEU PRO GLY ASP ASP SEQRES 20 A 585 THR PRO THR ASP ALA VAL VAL SER PRO SER ALA VAL THR SEQRES 21 A 585 VAL GLU THR ALA GLU THR LYS PRO MET ASP LYS GLN THR SEQRES 22 A 585 THR SER ARG SER LYS PRO ALA PRO ALA VAL ARG ALA ALA SEQRES 23 A 585 TYR ASP ASN GLU LEU VAL GLU ALA VAL LYS ARG PHE GLN SEQRES 24 A 585 ALA TRP GLN GLY LEU GLY ALA ASP GLY ALA ILE GLY PRO SEQRES 25 A 585 ALA THR ARG ASP TRP LEU ASN VAL THR PRO ALA GLN ARG SEQRES 26 A 585 ALA GLY VAL LEU ALA LEU ASN ILE GLN ARG LEU ARG LEU SEQRES 27 A 585 LEU PRO THR GLU LEU SER THR GLY ILE MET VAL ASN ILE SEQRES 28 A 585 PRO ALA TYR SER LEU VAL TYR TYR GLN ASN GLY ASN GLN SEQRES 29 A 585 VAL LEU ASP SER ARG VAL ILE VAL GLY ARG PRO ASP ARG SEQRES 30 A 585 LYS THR PRO MET MET SER SER ALA LEU ASN ASN VAL VAL SEQRES 31 A 585 VAL ASN PRO PRO TRP ASN VAL PRO PRO THR LEU ALA ARG SEQRES 32 A 585 LYS ASP ILE LEU PRO LYS VAL ARG ASN ASP PRO GLY TYR SEQRES 33 A 585 LEU GLU SER HIS GLY TYR THR VAL MET ARG GLY TRP ASN SEQRES 34 A 585 SER ARG GLU ALA ILE ASP PRO TRP GLN VAL ASP TRP SER SEQRES 35 A 585 THR ILE THR ALA SER ASN LEU PRO PHE ARG PHE GLN GLN SEQRES 36 A 585 ALA PRO GLY PRO ARG ASN SER LEU GLY ARG TYR LYS PHE SEQRES 37 A 585 ASN MET PRO SER SER GLU ALA ILE TYR LEU HIS ASP THR SEQRES 38 A 585 PRO ASN HIS ASN LEU PHE LYS ARG ASP THR ARG ALA LEU SEQRES 39 A 585 SER SER GLY CYS VAL ARG VAL ASN LYS ALA SER ASP LEU SEQRES 40 A 585 ALA ASN MET LEU LEU GLN ASP ALA GLY TRP ASN ASP LYS SEQRES 41 A 585 ARG ILE SER ASP ALA LEU LYS GLN GLY ASP THR ARG TYR SEQRES 42 A 585 VAL ASN ILE ARG GLN SER ILE PRO VAL ASN LEU TYR TYR SEQRES 43 A 585 LEU THR ALA PHE VAL GLY ALA ASP GLY ARG THR GLN TYR SEQRES 44 A 585 ARG THR ASP ILE TYR ASN TYR ASP LEU PRO ALA ARG SER SEQRES 45 A 585 SER SER GLN ILE VAL SER LYS ALA GLU GLN LEU ILE ARG HET MXR A 701 26 HET SO4 A 702 5 HET SO4 A 703 5 HET SO4 A 704 5 HET SO4 A 705 5 HET SO4 A 706 5 HETNAM MXR (2S,3R,4S)-4-{[(3S,5R)-5-(DIMETHYLCARBAMOYL)PYRROLIDIN- HETNAM 2 MXR 3-YL]SULFANYL}-2-[(2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL]- HETNAM 3 MXR 3-METHYL-3,4-DIHYDRO-2H-PYRROLE-5-CARBOXYLIC ACID HETNAM SO4 SULFATE ION HETSYN MXR MEROPENEM BOUND FORM (TAUTOMERISM) FORMUL 2 MXR C17 H27 N3 O5 S FORMUL 3 SO4 5(O4 S 2-) FORMUL 8 HOH *21(H2 O) HELIX 1 AA1 SER A 40 GLN A 47 1 8 HELIX 2 AA2 GLN A 77 LEU A 82 5 6 HELIX 3 AA3 TYR A 90 ARG A 101 1 12 HELIX 4 AA4 ASN A 109 GLY A 127 1 19 HELIX 5 AA5 PRO A 130 THR A 140 1 11 HELIX 6 AA6 GLY A 146 LEU A 175 1 30 HELIX 7 AA7 PRO A 187 LYS A 200 1 14 HELIX 8 AA8 GLN A 202 GLY A 209 1 8 HELIX 9 AA9 GLN A 216 ASP A 230 1 15 HELIX 10 AB1 ASP A 251 THR A 262 1 12 HELIX 11 AB2 ASP A 318 GLN A 332 1 15 HELIX 12 AB3 GLY A 341 VAL A 350 1 10 HELIX 13 AB4 THR A 351 LEU A 366 1 16 HELIX 14 AB5 ARG A 367 LEU A 369 5 3 HELIX 15 AB6 PRO A 428 ILE A 436 1 9 HELIX 16 AB7 ILE A 436 ARG A 441 1 6 HELIX 17 AB8 PRO A 444 HIS A 450 1 7 HELIX 18 AB9 ASP A 465 VAL A 469 5 5 HELIX 19 AC1 ASP A 470 ILE A 474 5 5 HELIX 20 AC2 ASN A 513 ARG A 519 5 7 HELIX 21 AC3 LYS A 533 ASP A 544 1 12 HELIX 22 AC4 ASN A 548 GLY A 559 1 12 HELIX 23 AC5 ILE A 606 ILE A 614 1 9 SHEET 1 AA1 6 MET A 412 ALA A 415 0 SHEET 2 AA1 6 PRO A 571 TYR A 575 -1 O VAL A 572 N SER A 414 SHEET 3 AA1 6 GLY A 376 ASN A 380 1 N ILE A 377 O PRO A 571 SHEET 4 AA1 6 SER A 385 GLN A 390 -1 O VAL A 387 N MET A 378 SHEET 5 AA1 6 ASN A 393 GLY A 403 -1 O ASN A 393 N GLN A 390 SHEET 6 AA1 6 ALA A 523 SER A 525 1 O SER A 525 N VAL A 402 SHEET 1 AA210 MET A 412 ALA A 415 0 SHEET 2 AA210 PRO A 571 TYR A 575 -1 O VAL A 572 N SER A 414 SHEET 3 AA210 GLY A 376 ASN A 380 1 N ILE A 377 O PRO A 571 SHEET 4 AA210 SER A 385 GLN A 390 -1 O VAL A 387 N MET A 378 SHEET 5 AA210 ASN A 393 GLY A 403 -1 O ASN A 393 N GLN A 390 SHEET 6 AA210 VAL A 529 VAL A 531 -1 O ARG A 530 N ILE A 401 SHEET 7 AA210 LEU A 508 HIS A 509 1 N HIS A 509 O VAL A 531 SHEET 8 AA210 TYR A 496 ASN A 499 -1 N PHE A 498 O LEU A 508 SHEET 9 AA210 ASN A 418 VAL A 421 -1 N VAL A 420 O LYS A 497 SHEET 10 AA210 ARG A 562 ASN A 565 -1 O VAL A 564 N VAL A 419 SHEET 1 AA3 3 TRP A 425 ASN A 426 0 SHEET 2 AA3 3 ARG A 482 GLN A 485 -1 O GLN A 485 N TRP A 425 SHEET 3 AA3 3 TYR A 452 MET A 455 -1 N THR A 453 O GLN A 484 SHEET 1 AA4 2 ALA A 579 VAL A 581 0 SHEET 2 AA4 2 THR A 587 TYR A 589 -1 O GLN A 588 N PHE A 580 LINK C1 MXR A 701 SG CYS A 528 1555 1555 0.89 SITE 1 AC1 7 PRO A 428 ALA A 505 ILE A 506 TYR A 507 SITE 2 AC1 7 HIS A 509 SER A 526 CYS A 528 SITE 1 AC2 3 SER A 177 LYS A 179 HOH A 803 SITE 1 AC3 5 LYS A 170 ARG A 173 TRP A 174 TYR A 181 SITE 2 AC3 5 ALA A 182 SITE 1 AC4 3 ARG A 519 ASP A 520 THR A 521 SITE 1 AC5 4 GLY A 341 PRO A 342 ALA A 343 THR A 344 SITE 1 AC6 3 ARG A 441 THR A 475 ALA A 476 CRYST1 126.499 126.499 88.801 90.00 90.00 90.00 P 43 21 2 8 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 0.007905 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007905 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011261 0.00000