HEADER HYDROLASE 20-MAY-14 4PMA
TITLE CRYSTAL STRUCTURE OF CTX-M-14 S70G:S237A:R276A BETA-LACTAMASE AT 1.39
TITLE 2 ANGSTROMS RESOLUTION
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: BETA-LACTAMASE CTX-M-14;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 29-291;
COMPND 5 ENGINEERED: YES;
COMPND 6 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE SUBSP. PNEUMONIAE;
SOURCE 3 ORGANISM_TAXID: 1125630;
SOURCE 4 STRAIN: HS11286;
SOURCE 5 GENE: KPHS_P301310;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS CLASS A BETA-LACTAMASE, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR A.M.CARDENAS,C.J.ADAMSKI,N.G.BROWN,L.B.HORTON,B.SANKARAN,T.PALZKILL
REVDAT 5 27-DEC-23 4PMA 1 REMARK
REVDAT 4 11-DEC-19 4PMA 1 REMARK
REVDAT 3 13-SEP-17 4PMA 1 SOURCE JRNL REMARK
REVDAT 2 04-MAR-15 4PMA 1 JRNL
REVDAT 1 31-DEC-14 4PMA 0
JRNL AUTH C.J.ADAMSKI,A.M.CARDENAS,N.G.BROWN,L.B.HORTON,B.SANKARAN,
JRNL AUTH 2 B.V.PRASAD,H.F.GILBERT,T.PALZKILL
JRNL TITL MOLECULAR BASIS FOR THE CATALYTIC SPECIFICITY OF THE CTX-M
JRNL TITL 2 EXTENDED-SPECTRUM BETA-LACTAMASES.
JRNL REF BIOCHEMISTRY V. 54 447 2015
JRNL REFN ISSN 0006-2960
JRNL PMID 25489790
JRNL DOI 10.1021/BI501195G
REMARK 2
REMARK 2 RESOLUTION. 1.40 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.4_486)
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) : 1.40
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.99
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3
REMARK 3 NUMBER OF REFLECTIONS : 44218
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.154
REMARK 3 R VALUE (WORKING SET) : 0.153
REMARK 3 FREE R VALUE : 0.181
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040
REMARK 3 FREE R VALUE TEST SET COUNT : 2228
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 24.9894 - 3.0131 1.00 4547 228 0.1580 0.1716
REMARK 3 2 3.0131 - 2.3922 1.00 4346 246 0.1614 0.1984
REMARK 3 3 2.3922 - 2.0900 0.99 4260 241 0.1488 0.1723
REMARK 3 4 2.0900 - 1.8989 0.99 4273 227 0.1466 0.1750
REMARK 3 5 1.8989 - 1.7629 0.98 4240 207 0.1517 0.2071
REMARK 3 6 1.7629 - 1.6590 0.97 4156 220 0.1441 0.1937
REMARK 3 7 1.6590 - 1.5759 0.97 4126 217 0.1434 0.1812
REMARK 3 8 1.5759 - 1.5073 0.96 4049 238 0.1412 0.1757
REMARK 3 9 1.5073 - 1.4493 0.95 4021 200 0.1498 0.1711
REMARK 3 10 1.4493 - 1.3993 0.93 3972 204 0.1605 0.1737
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
REMARK 3 SOLVENT RADIUS : 1.00
REMARK 3 SHRINKAGE RADIUS : 0.72
REMARK 3 K_SOL : 0.40
REMARK 3 B_SOL : 60.00
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.130
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.110
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -2.48630
REMARK 3 B22 (A**2) : 2.73250
REMARK 3 B33 (A**2) : -0.24610
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
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 : 0.006 1993
REMARK 3 ANGLE : 1.083 2716
REMARK 3 CHIRALITY : 0.064 322
REMARK 3 PLANARITY : 0.005 357
REMARK 3 DIHEDRAL : 11.979 727
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 4PMA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JUL-14.
REMARK 100 THE DEPOSITION ID IS D_1000201677.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 07-FEB-11
REMARK 200 TEMPERATURE (KELVIN) : 80
REMARK 200 PH : NULL
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) : 0.97
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL
REMARK 200 DATA SCALING SOFTWARE : NULL
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46446
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.390
REMARK 200 RESOLUTION RANGE LOW (A) : 25.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 200 DATA REDUNDANCY : 3.000
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 27.5000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
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 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 39.27
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, PEG 4000, VAPOR
REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 296K
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 20.87100
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.35050
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.19000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.35050
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.87100
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.19000
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 TOTAL BURIED SURFACE AREA: 390 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 10700 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 KCAL/MOL
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 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 -140.26 47.64
REMARK 500 VAL A 103 -135.35 -113.03
REMARK 500 SER A 220 -128.71 -102.12
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 SO4 A 301
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 302
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4PM5 RELATED DB: PDB
REMARK 900 RELATED ID: 4PM6 RELATED DB: PDB
REMARK 900 RELATED ID: 4PM7 RELATED DB: PDB
REMARK 900 RELATED ID: 4PM8 RELATED DB: PDB
REMARK 900 RELATED ID: 4PM9 RELATED DB: PDB
DBREF 4PMA A 25 290 UNP G8XD06 G8XD06_KLEPH 29 291
SEQADV 4PMA GLY A 70 UNP G8XD06 SER 73 ENGINEERED MUTATION
SEQADV 4PMA ALA A 237 UNP G8XD06 SER 240 ENGINEERED MUTATION
SEQADV 4PMA ALA A 276 UNP G8XD06 ARG 277 ENGINEERED MUTATION
SEQRES 1 A 263 GLN THR SER ALA VAL GLN GLN LYS LEU ALA ALA LEU GLU
SEQRES 2 A 263 LYS SER SER GLY GLY ARG LEU GLY VAL ALA LEU ILE ASP
SEQRES 3 A 263 THR ALA ASP ASN THR GLN VAL LEU TYR ARG GLY ASP GLU
SEQRES 4 A 263 ARG PHE PRO MET CYS GLY THR SER LYS VAL MET ALA ALA
SEQRES 5 A 263 ALA ALA VAL LEU LYS GLN SER GLU THR GLN LYS GLN LEU
SEQRES 6 A 263 LEU ASN GLN PRO VAL GLU ILE LYS PRO ALA ASP LEU VAL
SEQRES 7 A 263 ASN TYR ASN PRO ILE ALA GLU LYS HIS VAL ASN GLY THR
SEQRES 8 A 263 MET THR LEU ALA GLU LEU SER ALA ALA ALA LEU GLN TYR
SEQRES 9 A 263 SER ASP ASN THR ALA MET ASN LYS LEU ILE ALA GLN LEU
SEQRES 10 A 263 GLY GLY PRO GLY GLY VAL THR ALA PHE ALA ARG ALA ILE
SEQRES 11 A 263 GLY ASP GLU THR PHE ARG LEU ASP ARG THR GLU PRO THR
SEQRES 12 A 263 LEU ASN THR ALA ILE PRO GLY ASP PRO ARG ASP THR THR
SEQRES 13 A 263 THR PRO ARG ALA MET ALA GLN THR LEU ARG GLN LEU THR
SEQRES 14 A 263 LEU GLY HIS ALA LEU GLY GLU THR GLN ARG ALA GLN LEU
SEQRES 15 A 263 VAL THR TRP LEU LYS GLY ASN THR THR GLY ALA ALA SER
SEQRES 16 A 263 ILE ARG ALA GLY LEU PRO THR SER TRP THR VAL GLY ASP
SEQRES 17 A 263 LYS THR GLY ALA GLY ASP TYR GLY THR THR ASN ASP ILE
SEQRES 18 A 263 ALA VAL ILE TRP PRO GLN GLY ARG ALA PRO LEU VAL LEU
SEQRES 19 A 263 VAL THR TYR PHE THR GLN PRO GLN GLN ASN ALA GLU SER
SEQRES 20 A 263 ARG ALA ASP VAL LEU ALA SER ALA ALA ARG ILE ILE ALA
SEQRES 21 A 263 GLU GLY LEU
HET SO4 A 301 5
HET SO4 A 302 5
HETNAM SO4 SULFATE ION
FORMUL 2 SO4 2(O4 S 2-)
FORMUL 4 HOH *349(H2 O)
HELIX 1 AA1 SER A 27 GLY A 41 1 15
HELIX 2 AA2 CYS A 69 THR A 71 5 3
HELIX 3 AA3 SER A 72 GLU A 85 1 14
HELIX 4 AA4 GLN A 89 ASN A 92 5 4
HELIX 5 AA5 LYS A 98 LEU A 102 5 5
HELIX 6 AA6 ILE A 108 VAL A 113 5 6
HELIX 7 AA7 LEU A 119 SER A 130 1 12
HELIX 8 AA8 ASP A 131 LEU A 142 1 12
HELIX 9 AA9 GLY A 144 ILE A 155 1 12
HELIX 10 AB1 PRO A 167 THR A 171 5 5
HELIX 11 AB2 THR A 182 LEU A 195 1 14
HELIX 12 AB3 GLY A 200 GLY A 213 1 14
HELIX 13 AB4 SER A 220 LEU A 225 5 6
HELIX 14 AB5 ARG A 275 GLU A 288 1 14
SHEET 1 AA1 5 THR A 55 TYR A 60 0
SHEET 2 AA1 5 ARG A 43 ASP A 50 -1 N ASP A 50 O THR A 55
SHEET 3 AA1 5 LEU A 259 THR A 266 -1 O TYR A 264 N GLY A 45
SHEET 4 AA1 5 THR A 243 TRP A 251 -1 N ILE A 250 O LEU A 259
SHEET 5 AA1 5 THR A 230 GLY A 238 -1 N THR A 230 O TRP A 251
SHEET 1 AA2 2 PHE A 66 PRO A 67 0
SHEET 2 AA2 2 THR A 180 THR A 181 -1 O THR A 181 N PHE A 66
SHEET 1 AA3 2 PRO A 94 ILE A 97 0
SHEET 2 AA3 2 GLY A 115 THR A 118 -1 O GLY A 115 N ILE A 97
CISPEP 1 GLU A 166 PRO A 167 0 4.28
SITE 1 AC1 11 GLY A 70 LYS A 73 SER A 130 ASN A 132
SITE 2 AC1 11 LYS A 234 GLY A 236 ALA A 237 HOH A 554
SITE 3 AC1 11 HOH A 579 HOH A 598 HOH A 604
SITE 1 AC2 8 ILE A 108 LYS A 111 HIS A 112 HOH A 406
SITE 2 AC2 8 HOH A 422 HOH A 435 HOH A 446 HOH A 710
CRYST1 41.742 62.380 86.701 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 0.023957 0.000000 0.000000 0.00000
SCALE2 0.000000 0.016031 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011534 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
