HEADER HYDROLASE/HYDROLASE INHIBITOR 05-JUN-18 6DMH TITLE A MULTICONFORMER LIGAND MODEL OF ACYLENZYME INTERMEDIATE OF MEROPENEM TITLE 2 BOUND TO AN SFC-1 E166A MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.5.2.6; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SERRATIA FONTICOLA; SOURCE 3 ORGANISM_TAXID: 47917; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS COMPLEX, MULTI CONFORMER MODEL, ANTIBIOTIC, HYDROLASE, HYDROLASE- KEYWDS 2 HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.M.HUDSON,G.VAN ZUNDERT,D.KEEDY,R.FONSECA,A.HELIOU,P.SURESH, AUTHOR 2 K.BORRELLI,T.DAY,J.S.FRASER,H.VAN DEN BEDEM REVDAT 2 24-APR-19 6DMH 1 JRNL REVDAT 1 19-DEC-18 6DMH 0 JRNL AUTH G.C.P.VAN ZUNDERT,B.M.HUDSON,S.H.P.DE OLIVEIRA,D.A.KEEDY, JRNL AUTH 2 R.FONSECA,A.HELIOU,P.SURESH,K.BORRELLI,T.DAY,J.S.FRASER, JRNL AUTH 3 H.VAN DEN BEDEM JRNL TITL QFIT-LIGAND REVEALS WIDESPREAD CONFORMATIONAL HETEROGENEITY JRNL TITL 2 OF DRUG-LIKE MOLECULES IN X-RAY ELECTRON DENSITY MAPS. JRNL REF J. MED. CHEM. V. 61 11183 2018 JRNL REFN ISSN 1520-4804 JRNL PMID 30457858 JRNL DOI 10.1021/ACS.JMEDCHEM.8B01292 REMARK 0 REMARK 0 THIS ENTRY 6DMH REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL REMARK 0 DATA IN 4EV4, DETERMINED BY F.FONSECA,E.I.CHUDYK,M.W.VAN DER REMARK 0 KAMP,A.CORREIA,A.J.MULHOLLAND,J.SPENCER REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH F.FONSECA,E.I.CHUDYK,M.W.VAN DER KAMP,A.CORREIA, REMARK 1 AUTH 2 A.J.MULHOLLAND,J.SPENCER REMARK 1 TITL THE BASIS FOR CARBAPENEM HYDROLYSIS BY CLASS A REMARK 1 TITL 2 BETA-LACTAMASES: A COMBINED INVESTIGATION USING REMARK 1 TITL 3 CRYSTALLOGRAPHY AND SIMULATIONS. REMARK 1 REF J. AM. CHEM. SOC. V. 134 18275 2012 REMARK 1 REFN ESSN 1520-5126 REMARK 1 PMID 23030300 REMARK 1 DOI 10.1021/JA304460J REMARK 2 REMARK 2 RESOLUTION. 1.30 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.500 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 68360 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.117 REMARK 3 R VALUE (WORKING SET) : 0.116 REMARK 3 FREE R VALUE : 0.143 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.920 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 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 33.3556 - 3.1316 1.00 5285 164 0.1363 0.1539 REMARK 3 2 3.1316 - 2.4859 1.00 5098 148 0.1279 0.1426 REMARK 3 3 2.4859 - 2.1717 1.00 5056 154 0.1109 0.1198 REMARK 3 4 2.1717 - 1.9732 1.00 5018 147 0.1154 0.1551 REMARK 3 5 1.9732 - 1.8318 1.00 4990 153 0.1129 0.1500 REMARK 3 6 1.8318 - 1.7238 1.00 5004 150 0.1075 0.1321 REMARK 3 7 1.7238 - 1.6375 1.00 4986 153 0.0973 0.1401 REMARK 3 8 1.6375 - 1.5662 1.00 4977 144 0.0916 0.1296 REMARK 3 9 1.5662 - 1.5059 1.00 4975 141 0.0909 0.1308 REMARK 3 10 1.5059 - 1.4539 0.99 4903 151 0.0932 0.1289 REMARK 3 11 1.4539 - 1.4085 0.95 4678 156 0.0976 0.1338 REMARK 3 12 1.4085 - 1.3682 0.88 4413 111 0.1057 0.1449 REMARK 3 13 1.3682 - 1.3322 0.77 3818 132 0.1197 0.1665 REMARK 3 14 1.3322 - 1.2997 0.64 3160 95 0.1391 0.1867 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 12.000 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.59 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 : 0.010 2386 REMARK 3 ANGLE : 1.370 3268 REMARK 3 CHIRALITY : 0.091 364 REMARK 3 PLANARITY : 0.009 430 REMARK 3 DIHEDRAL : 14.861 915 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 6DMH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1000234850. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUL-09 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 : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97630 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 68435 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 200 DATA REDUNDANCY : 11.90 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 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: NULL REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: AUTHOR USED THE SF DATA FROM ENTRY 4EV4 REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NA ACETATE, PEG 3350, PH 7, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 29.59250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.56350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.97750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.56350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.59250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.97750 REMARK 290 SMTRY3 4 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 SER A 70 N CA C O CB OG 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 O ALA A 22 HD22 ASN A 291 1.49 REMARK 500 HD21 ASN A 197 O HOH A 404 1.57 REMARK 500 OD1 ASP A 209 O HOH A 401 1.77 REMARK 500 OE1 GLU A 110 O HOH A 402 1.79 REMARK 500 O HOH A 635 O HOH A 745 1.92 REMARK 500 O HOH A 515 O HOH A 721 1.95 REMARK 500 O HOH A 648 O HOH A 759 1.96 REMARK 500 O HOH A 488 O HOH A 532 1.96 REMARK 500 O HOH A 655 O HOH A 712 1.99 REMARK 500 ND2 ASN A 197 O HOH A 404 2.01 REMARK 500 O HOH A 678 O HOH A 757 2.01 REMARK 500 O HOH A 661 O HOH A 707 2.02 REMARK 500 O HOH A 414 O HOH A 516 2.05 REMARK 500 O HOH A 678 O HOH A 769 2.07 REMARK 500 OD2 ASP A 50 OG SER A 53 2.09 REMARK 500 OH1 HAR A 100 OE1 GLU A 103 2.12 REMARK 500 OD1 ASN A 38 O HOH A 405 2.15 REMARK 500 NZ LYS A 267 O HOH A 406 2.16 REMARK 500 O HOH A 654 O HOH A 690 2.17 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 O HOH A 745 O HOH A 780 3545 2.03 REMARK 500 O HOH A 644 O HOH A 773 3555 2.03 REMARK 500 O HOH A 402 O HOH A 617 2455 2.11 REMARK 500 O HOH A 496 O HOH A 563 4545 2.12 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 204 NE - CZ - NH1 ANGL. DEV. = -7.1 DEGREES REMARK 500 ARG A 204 NE - CZ - NH2 ANGL. DEV. = 4.4 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 CYS A 69 -146.16 52.68 REMARK 500 CYS A 69 -148.66 52.68 REMARK 500 TYR A 97 41.89 -148.79 REMARK 500 ARG A 220 -121.54 -116.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 836 DISTANCE = 6.34 ANGSTROMS REMARK 525 HOH A 837 DISTANCE = 6.38 ANGSTROMS REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 HOH A 403 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MER A 305 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4EV4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SERRATIA FONTICOLA CARBAPENEMASE SFC-1 E166A REMARK 900 MUTANT WITH THE ACYLENZYME INTERMEDIATE OF MEROPENEM DBREF 6DMH A 22 292 UNP Q6JP75 Q6JP75_SERFO 27 296 SEQADV 6DMH ALA A 166 UNP Q6JP75 GLU 171 ENGINEERED MUTATION SEQADV 6DMH ALA A 255 UNP Q6JP75 GLY 259 CONFLICT SEQADV 6DMH ARG A 270 UNP Q6JP75 LYS 274 CONFLICT SEQRES 1 A 270 ALA SER GLN PRO PRO GLN VAL THR VAL ASP LYS LEU LYS SEQRES 2 A 270 ARG LEU GLU ASN ASP PHE GLY GLY ARG ILE GLY VAL TYR SEQRES 3 A 270 ALA ILE ASP THR GLY SER ASN LYS THR PHE GLY TYR ARG SEQRES 4 A 270 ALA ASN GLU ARG PHE PRO LEU CYS SER SER PHE LYS GLY SEQRES 5 A 270 PHE LEU ALA ALA ALA VAL LEU SER LYS SER GLN GLN GLN SEQRES 6 A 270 GLU GLY LEU LEU ASN GLN ARG ILE ARG TYR ASP ASN HAR SEQRES 7 A 270 VAL MET GLU PRO HIS SER PRO VAL THR GLU LYS GLN ILE SEQRES 8 A 270 THR THR GLY MET THR VAL ALA GLU LEU SER ALA ALA THR SEQRES 9 A 270 LEU GLN TYR SER ASP ASN GLY ALA ALA ASN LEU LEU LEU SEQRES 10 A 270 GLU LYS LEU ILE GLY GLY PRO GLU GLY MET THR SER PHE SEQRES 11 A 270 MET ARG SER ILE GLY ASP ASN VAL PHE ARG LEU ASP ARG SEQRES 12 A 270 TRP ALA LEU GLU LEU ASN SER ALA ILE PRO GLY ASP ASP SEQRES 13 A 270 ARG ASP THR SER THR PRO LYS ALA VAL ALA GLU SER MET SEQRES 14 A 270 GLN LYS LEU ALA PHE GLY ASN VAL LEU GLY LEU THR GLU SEQRES 15 A 270 ARG HIS GLN LEU MET ASP TRP PHE LYS GLY ASN THR THR SEQRES 16 A 270 GLY GLY ALA ARG ILE ARG ALA SER VAL PRO ALA ASN TRP SEQRES 17 A 270 VAL VAL GLY ASP LYS THR GLY THR CYS GLY VAL TYR GLY SEQRES 18 A 270 THR ALA ASN ASP TYR ALA VAL ILE TRP PRO VAL ALA HIS SEQRES 19 A 270 ALA PRO ILE VAL LEU ALA VAL TYR THR SER LYS PRO ASP SEQRES 20 A 270 ARG ASN SER LYS HIS SER ASP ALA VAL ILE ALA ASP ALA SEQRES 21 A 270 SER ARG ILE VAL LEU GLU SER PHE ASN ILE MODRES 6DMH HAR A 100 ARG MODIFIED RESIDUE HET HAR A 100 40 HET EDO A 301 10 HET EDO A 302 10 HET EDO A 303 10 HET EDO A 304 10 HET MER A 305 100 HETNAM HAR N-OMEGA-HYDROXY-L-ARGININE HETNAM EDO 1,2-ETHANEDIOL HETNAM MER (4R,5S)-3-{[(3S,5S)-5-(DIMETHYLCARBAMOYL)PYRROLIDIN-3- HETNAM 2 MER YL]SULFANYL}-5-[(2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL]-4- HETNAM 3 MER METHYL-4,5-DIHYDRO-1H-PYRROLE-2-CARBOXYLIC ACID HETSYN EDO ETHYLENE GLYCOL HETSYN MER MEROPENEM, BOUND FORM FORMUL 1 HAR C6 H14 N4 O3 FORMUL 2 EDO 4(C2 H6 O2) FORMUL 6 MER C17 H27 N3 O5 S FORMUL 7 HOH *437(H2 O) HELIX 1 AA1 PRO A 25 GLY A 41 1 17 HELIX 2 AA2 SER A 71 GLN A 87 1 17 HELIX 3 AA3 GLY A 89 ASN A 92 5 4 HELIX 4 AA4 VAL A 108 GLN A 112 5 5 HELIX 5 AA5 VAL A 119 SER A 130 1 12 HELIX 6 AA6 ASP A 131 LEU A 141 1 12 HELIX 7 AA7 GLY A 143 ILE A 155 1 13 HELIX 8 AA8 LEU A 167 SER A 171 5 5 HELIX 9 AA9 THR A 182 GLY A 196 1 15 HELIX 10 AB1 GLY A 200 GLY A 213 1 14 HELIX 11 AB2 ARG A 220 VAL A 225 5 6 HELIX 12 AB3 SER A 275 PHE A 290 1 16 SHEET 1 AA1 5 THR A 56 TYR A 60 0 SHEET 2 AA1 5 ARG A 43 ASP A 50 -1 N VAL A 46 O TYR A 60 SHEET 3 AA1 5 ILE A 259 SER A 266 -1 O TYR A 264 N GLY A 45 SHEET 4 AA1 5 ALA A 244 TRP A 251 -1 N ASP A 246 O VAL A 263 SHEET 5 AA1 5 VAL A 230 THR A 237 -1 N VAL A 230 O TRP A 251 SHEET 1 AA2 2 PHE A 66 PRO A 67 0 SHEET 2 AA2 2 THR A 180 SER A 181 -1 O SER A 181 N PHE A 66 SHEET 1 AA3 2 ARG A 94 ILE A 95 0 SHEET 2 AA3 2 MET A 117 THR A 118 -1 O MET A 117 N ILE A 95 SSBOND 1 CYS A 69 CYS A 238 1555 1555 2.08 LINK C ASN A 99 N HAR A 100 1555 1555 1.33 LINK C HAR A 100 N VAL A 101 1555 1555 1.34 SITE 1 AC1 6 PHE A 57 SER A 289 HOH A 445 HOH A 475 SITE 2 AC1 6 HOH A 484 HOH A 584 SITE 1 AC2 6 GLY A 156 ASN A 158 ALA A 185 GLU A 188 SITE 2 AC2 6 HOH A 507 HOH A 508 SITE 1 AC3 5 ARG A 94 GLN A 112 THR A 115 GLY A 116 SITE 2 AC3 5 GLU A 121 SITE 1 AC4 7 ARG A 61 ALA A 62 ASN A 63 GLU A 64 SITE 2 AC4 7 HAR A 100 HOH A 454 HOH A 617 SITE 1 AC5 15 CYS A 69 SER A 70 SER A 130 ASN A 132 SITE 2 AC5 15 ASN A 170 THR A 216 LYS A 234 THR A 235 SITE 3 AC5 15 GLY A 236 THR A 237 HOH A 420 HOH A 547 SITE 4 AC5 15 HOH A 548 HOH A 579 HOH A 665 CRYST1 59.185 61.955 79.127 90.00 90.00 90.00 P 21 21 21 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 0.016896 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016141 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012638 0.00000