HEADER TRANSFERASE 17-OCT-20 7KGM TITLE C. RODENTIUM YCBB - ERTAPENEM COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE EXPORTED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CITROBACTER RODENTIUM (STRAIN ICC168); SOURCE 3 ORGANISM_TAXID: 637910; SOURCE 4 STRAIN: ICC168; SOURCE 5 GENE: ROD_09941; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS L, D-TRANSPEPTIDASE, ANTIBIOTIC, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR N.A.CAVENEY,N.C.J.STRYNADKA REVDAT 3 18-OCT-23 7KGM 1 REMARK REVDAT 2 03-FEB-21 7KGM 1 JRNL REVDAT 1 25-NOV-20 7KGM 0 JRNL AUTH N.A.CAVENEY,A.SERAPIO-PALACIOS,S.E.WOODWARD,T.BOZORGMEHR, JRNL AUTH 2 G.CABALLERO,M.VUCKOVIC,W.DENG,B.B.FINLAY,N.C.J.STRYNADKA JRNL TITL STRUCTURAL AND CELLULAR INSIGHTS INTO THE L,D-TRANSPEPTIDASE JRNL TITL 2 YCBB AS A THERAPEUTIC TARGET IN CITROBACTER RODENTIUM, JRNL TITL 3 SALMONELLA TYPHIMURIUM, AND SALMONELLA TYPHI INFECTIONS. JRNL REF ANTIMICROB.AGENTS CHEMOTHER. V. 65 2021 JRNL REFN ESSN 1098-6596 JRNL PMID 33139287 JRNL DOI 10.1128/AAC.01592-20 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 20707 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 1029 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 35.9700 - 4.9715 1.00 2932 155 0.1846 0.2046 REMARK 3 2 4.9715 - 3.9469 0.99 2824 148 0.1874 0.2081 REMARK 3 3 3.9469 - 3.4482 1.00 2825 144 0.2158 0.3354 REMARK 3 4 3.4482 - 3.1330 0.99 2805 134 0.2492 0.3653 REMARK 3 5 3.1330 - 2.9085 1.00 2755 170 0.3098 0.3631 REMARK 3 6 2.9085 - 2.7371 1.00 2767 137 0.3507 0.4617 REMARK 3 7 2.7371 - 2.6000 0.99 2770 141 0.3972 0.4119 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) : 0.430 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.910 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 52.68 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 61.60 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7KGM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-OCT-20. REMARK 100 THE DEPOSITION ID IS D_1000252441. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08B1-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20707 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 42.876 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.43000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.5700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.67 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: 6NTW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: C. RODENTIUM YCBB WAS CRYSTALLIZED AT REMARK 280 20C BY SITTING DROP VAPOUR DIFFUSION USING 0.2 UL PROTEIN REMARK 280 SOLUTION (8.8 MG/ML PURIFIED PROTEIN IN BUFFER A) AND 0.1 UL OF REMARK 280 MOTHER LIQUOR (0.16 M CALCIUM ACETATE, 0.08 M SODIUM CACODYLATE REMARK 280 PH 6.5, 14% (V/V) PEG 8K, 20% (V/V) GLYCEROL) WITH THE ADDITION REMARK 280 OF 1MM ERTAPENEM., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 298.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.59250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.59250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 44.99850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 58.85250 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 44.99850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 58.85250 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 62.59250 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 44.99850 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 58.85250 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 62.59250 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 44.99850 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 58.85250 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 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 48 REMARK 465 GLU A 49 REMARK 465 PRO A 50 REMARK 465 GLU A 51 REMARK 465 ILE A 52 REMARK 465 VAL A 53 REMARK 465 PRO A 54 REMARK 465 SER A 55 REMARK 465 ASP A 56 REMARK 465 SER A 57 REMARK 465 SER A 58 REMARK 465 ALA A 59 REMARK 465 ILE A 60 REMARK 465 MET A 61 REMARK 465 GLY A 62 REMARK 465 ALA A 63 REMARK 465 GLN A 64 REMARK 465 PRO A 65 REMARK 465 THR A 66 REMARK 465 SER A 67 REMARK 465 LEU A 68 REMARK 465 SER A 69 REMARK 465 GLN A 70 REMARK 465 PRO A 71 REMARK 465 ASP A 288 REMARK 465 GLY A 289 REMARK 465 GLY A 290 REMARK 465 PRO A 291 REMARK 465 LYS A 292 REMARK 465 ILE A 293 REMARK 465 ALA A 294 REMARK 465 LEU A 295 REMARK 465 PRO A 296 REMARK 465 GLY A 297 REMARK 465 ASP A 298 REMARK 465 ASP A 299 REMARK 465 ALA A 300 REMARK 465 GLN A 301 REMARK 465 ASN A 302 REMARK 465 VAL A 303 REMARK 465 VAL A 304 REMARK 465 VAL A 305 REMARK 465 SER A 306 REMARK 465 PRO A 307 REMARK 465 SER A 308 REMARK 465 ALA A 309 REMARK 465 PRO A 310 REMARK 465 VAL A 311 REMARK 465 LYS A 312 REMARK 465 GLU A 313 REMARK 465 LYS A 314 REMARK 465 GLN A 315 REMARK 465 ALA A 316 REMARK 465 ALA A 317 REMARK 465 VAL A 318 REMARK 465 VAL A 319 REMARK 465 SER A 320 REMARK 465 ASN A 321 REMARK 465 LYS A 322 REMARK 465 GLY A 466 REMARK 465 TRP A 467 REMARK 465 ASN A 468 REMARK 465 SER A 512 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 ND2 ASN A 557 NH2 ARG A 560 0.54 REMARK 500 OD1 ASN A 557 CZ ARG A 560 1.01 REMARK 500 OD1 ASN A 557 NH1 ARG A 560 1.05 REMARK 500 CG ASN A 557 CZ ARG A 560 1.21 REMARK 500 ND2 ASN A 557 CZ ARG A 560 1.49 REMARK 500 CG ASN A 557 NH2 ARG A 560 1.53 REMARK 500 OD1 ASN A 557 NE ARG A 560 1.59 REMARK 500 CG ASN A 557 NH1 ARG A 560 1.89 REMARK 500 CG ASN A 557 NE ARG A 560 1.93 REMARK 500 NH1 ARG A 123 OE1 GLN A 217 2.03 REMARK 500 OE1 GLN A 373 NH1 ARG A 376 2.06 REMARK 500 OD1 ASN A 557 NH2 ARG A 560 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 PRO A 510 N PRO A 510 CA 0.208 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 ARG A 195 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 195 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 PRO A 510 C - N - CA ANGL. DEV. = 18.0 DEGREES REMARK 500 PRO A 510 CA - N - CD ANGL. DEV. = -9.1 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 ASP A 92 -100.16 -63.22 REMARK 500 ILE A 93 -18.55 -158.59 REMARK 500 MET A 125 14.45 54.29 REMARK 500 ASN A 131 96.75 -69.96 REMARK 500 ALA A 262 -7.56 74.50 REMARK 500 ALA A 345 74.19 -102.76 REMARK 500 ALA A 380 -11.45 73.88 REMARK 500 GLU A 381 45.69 -140.70 REMARK 500 THR A 384 76.17 61.94 REMARK 500 SER A 422 117.06 -163.71 REMARK 500 SER A 423 -159.68 -152.49 REMARK 500 LEU A 488 109.92 -51.82 REMARK 500 LYS A 542 31.19 -89.16 REMARK 500 ALA A 609 -159.94 -76.83 REMARK 500 ARG A 610 34.01 75.79 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 ASP A 92 ILE A 93 114.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 1RG A 801 DBREF 7KGM A 48 622 UNP D2TS62 D2TS62_CITRI 48 622 SEQRES 1 A 575 ASP GLU PRO GLU ILE VAL PRO SER ASP SER SER ALA ILE SEQRES 2 A 575 MET GLY ALA GLN PRO THR SER LEU SER GLN PRO LEU GLU SEQRES 3 A 575 GLN SER PRO VAL THR GLY ILE MET ALA GLY ILE LYS PRO SEQRES 4 A 575 LEU PRO GLU GLY ILE ASP ILE GLY SER VAL ARG GLN GLN SEQRES 5 A 575 LEU LEU THR GLY LEU PRO SER GLY TYR THR PRO ALA TYR SEQRES 6 A 575 MET ASP GLN LEU THR LEU LEU TYR ALA ALA ARG GLU MET SEQRES 7 A 575 LYS PRO MET TRP GLU ASN ARG ASP ALA VAL ARG ALA PHE SEQRES 8 A 575 GLN GLN GLN LEU ALA GLU VAL ALA ILE ALA GLY PHE GLN SEQRES 9 A 575 PRO GLN PHE THR ARG TRP VAL GLU LEU LEU THR ASP PRO SEQRES 10 A 575 ALA VAL SER GLY GLN ALA ARG ASP VAL VAL LEU SER ASP SEQRES 11 A 575 ALA MET MET GLY TYR LEU GLN PHE VAL ALA GLY ILE PRO SEQRES 12 A 575 VAL ASN GLY ASN ARG TRP LEU TYR SER ASN LYS PRO TYR SEQRES 13 A 575 LYS LEU ALA THR PRO ALA LEU SER VAL ILE ASN GLN TRP SEQRES 14 A 575 GLN LEU ALA LEU ASP ASN GLY GLU LEU PRO ARG PHE ILE SEQRES 15 A 575 ALA SER LEU ALA PRO ALA HIS PRO GLN TYR ALA ARG MET SEQRES 16 A 575 HIS GLN SER LEU LEU ALA LEU VAL GLY ASP SER ARG PRO SEQRES 17 A 575 TRP PRO GLN LEU ARG SER ALA ALA THR LEU ARG PRO GLY SEQRES 18 A 575 GLN TRP SER SER ASP VAL PRO ALA LEU ARG GLU ILE LEU SEQRES 19 A 575 LYS ARG SER GLY MET LEU ASP GLY GLY PRO LYS ILE ALA SEQRES 20 A 575 LEU PRO GLY ASP ASP ALA GLN ASN VAL VAL VAL SER PRO SEQRES 21 A 575 SER ALA PRO VAL LYS GLU LYS GLN ALA ALA VAL VAL SER SEQRES 22 A 575 ASN LYS PRO ALA ALA TYR ASP ARG GLU LEU VAL ALA ALA SEQRES 23 A 575 VAL LYS GLN PHE GLN ALA TRP GLN GLY LEU GLY ALA ASP SEQRES 24 A 575 GLY ALA ILE GLY PRO ALA THR ARG TYR TRP MET ASN VAL SEQRES 25 A 575 THR PRO ALA GLN ARG ALA GLY GLY LEU ALA LEU ASN ILE SEQRES 26 A 575 GLN ARG LEU ARG LEU LEU PRO ALA GLU LEU SER THR GLY SEQRES 27 A 575 ILE MET VAL ASN ILE PRO ALA TYR SER LEU VAL TYR TYR SEQRES 28 A 575 GLN ASN GLY SER GLN VAL LEU ALA SER ARG VAL ILE VAL SEQRES 29 A 575 GLY ARG PRO ASP ARG LYS THR PRO MET MET SER SER ALA SEQRES 30 A 575 LEU ASN ASN VAL VAL VAL ASN PRO PRO TRP ASN VAL PRO SEQRES 31 A 575 PRO THR LEU ALA ARG LYS ASP ILE LEU PRO LYS LEU TRP SEQRES 32 A 575 ASN ASP PRO GLY TYR LEU GLU ARG HIS GLY TYR THR VAL SEQRES 33 A 575 MET ARG GLY TRP ASN SER LYS ASP ALA ILE ASP PRO TRP SEQRES 34 A 575 GLN VAL ASP TRP SER THR ILE THR PRO SER ASN LEU PRO SEQRES 35 A 575 PHE ARG PHE GLN GLN ALA PRO GLY ALA HIS ASN SER LEU SEQRES 36 A 575 GLY ARG TYR LYS PHE ASN MET PRO SER SER ASP ALA ILE SEQRES 37 A 575 TYR LEU HIS ASP THR PRO ASN HIS THR LEU PHE SER LYS SEQRES 38 A 575 ASP ALA ARG ALA LEU SER SER GLY CYS VAL ARG VAL ASN SEQRES 39 A 575 LYS ALA SER GLU LEU ALA ASN MET LEU LEU GLN ASP ALA SEQRES 40 A 575 GLY TRP ASN ASP THR ARG ILE SER ASP ALA LEU LYS GLN SEQRES 41 A 575 GLY ASN THR ARG TYR VAL THR ILE ARG GLN THR ILE PRO SEQRES 42 A 575 VAL ASN LEU TYR TYR LEU THR ALA PHE VAL GLY ALA ASP SEQRES 43 A 575 GLY ARG THR GLN TYR ARG THR ASP ILE TYR ASN TYR ASP SEQRES 44 A 575 LEU THR ALA ARG SER SER ALA GLN ILE VAL GLU LYS ALA SEQRES 45 A 575 GLU GLN LEU HET 1RG A 801 9 HETNAM 1RG (4R,5S)-3-({(3S,5S)-5-[(3-CARBOXYPHENYL) HETNAM 2 1RG CARBAMOYL]PYRROLIDIN-3-YL}SULFANYL)-5-[(1S,2R)-1- HETNAM 3 1RG FORMYL-2-HYDROXYPROPYL]-4-METHYL-4,5-DIHYDRO-1H- HETNAM 4 1RG PYRROLE-2-CARBOXYLIC ACID HETSYN 1RG ERTAPENEM, BOUND FORM PRE-ISOMERIZED FORMUL 2 1RG C22 H27 N3 O7 S FORMUL 3 HOH *10(H2 O) HELIX 1 AA1 SER A 75 ALA A 82 1 8 HELIX 2 AA2 SER A 95 THR A 102 1 8 HELIX 3 AA3 TYR A 112 ARG A 123 1 12 HELIX 4 AA4 ASN A 131 GLY A 149 1 19 HELIX 5 AA5 GLN A 151 THR A 162 1 12 HELIX 6 AA6 GLY A 168 LEU A 197 1 30 HELIX 7 AA7 ALA A 209 GLY A 223 1 15 HELIX 8 AA8 GLU A 224 LEU A 232 1 9 HELIX 9 AA9 GLN A 238 ASP A 252 1 15 HELIX 10 AB1 ASP A 273 SER A 284 1 12 HELIX 11 AB2 ASP A 327 GLN A 341 1 15 HELIX 12 AB3 GLY A 350 ASN A 358 1 9 HELIX 13 AB4 THR A 360 LEU A 375 1 16 HELIX 14 AB5 ARG A 376 LEU A 378 5 3 HELIX 15 AB6 ARG A 413 LYS A 417 5 5 HELIX 16 AB7 PRO A 437 ASP A 444 1 8 HELIX 17 AB8 ILE A 445 LEU A 449 5 5 HELIX 18 AB9 GLY A 454 HIS A 459 1 6 HELIX 19 AC1 ASP A 479 ILE A 483 5 5 HELIX 20 AC2 ASN A 522 LYS A 528 5 7 HELIX 21 AC3 LYS A 542 ALA A 554 1 13 HELIX 22 AC4 ASN A 557 GLY A 568 1 12 HELIX 23 AC5 GLN A 614 GLU A 620 1 7 SHEET 1 AA110 MET A 421 ALA A 424 0 SHEET 2 AA110 PRO A 580 TYR A 584 -1 O VAL A 581 N SER A 423 SHEET 3 AA110 ILE A 386 ASN A 389 1 N VAL A 388 O ASN A 582 SHEET 4 AA110 SER A 394 GLN A 399 -1 O VAL A 396 N MET A 387 SHEET 5 AA110 SER A 402 ILE A 410 -1 O SER A 407 N LEU A 395 SHEET 6 AA110 VAL A 538 VAL A 540 -1 O ARG A 539 N ILE A 410 SHEET 7 AA110 LEU A 517 HIS A 518 1 N HIS A 518 O VAL A 540 SHEET 8 AA110 TYR A 505 ASN A 508 -1 N PHE A 507 O LEU A 517 SHEET 9 AA110 ASN A 427 VAL A 430 -1 N VAL A 429 O LYS A 506 SHEET 10 AA110 ARG A 571 THR A 574 -1 O ARG A 571 N VAL A 430 SHEET 1 AA2 4 TRP A 434 ASN A 435 0 SHEET 2 AA2 4 ARG A 491 GLN A 494 -1 O GLN A 494 N TRP A 434 SHEET 3 AA2 4 TYR A 461 MET A 464 -1 N MET A 464 O ARG A 491 SHEET 4 AA2 4 ALA A 472 ILE A 473 -1 O ILE A 473 N VAL A 463 SHEET 1 AA3 2 ALA A 588 VAL A 590 0 SHEET 2 AA3 2 THR A 596 TYR A 598 -1 O GLN A 597 N PHE A 589 LINK SG CYS A 537 CAA 1RG A 801 1555 1555 1.81 CRYST1 89.997 117.705 125.185 90.00 90.00 90.00 C 2 2 21 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 0.011112 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008496 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007988 0.00000