HEADER HYDROLASE 14-SEP-22 8B2W TITLE MILLISECOND CRYO-TRAPPING BY THE SPITROBOT CRYSTAL PLUNGER, CTX-M-14 TITLE 2 E166A, AMPICILLIN, 500 MS COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.5.2.6; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 573; SOURCE 4 GENE: CTX-M-14; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BETA-LACTAMASE, CTX-M-14, TIME-RESOLVED CRYSTALLOGRAPHY, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR P.MEHRABI,S.SUNG,D.VON STETTEN,A.PRESTER,C.E.HATTON,S.KLEINE-DOEPKE, AUTHOR 2 A.BERKES,G.GORE,J.P.LEIMKOHL,H.SCHIKORA,M.KOLLEWE,H.ROHDE, AUTHOR 3 M.WILMANNS,F.TELLKAMP,E.C.SCHULZ REVDAT 2 07-FEB-24 8B2W 1 REMARK REVDAT 1 24-MAY-23 8B2W 0 JRNL AUTH P.MEHRABI,S.SUNG,D.VON STETTEN,A.PRESTER,C.E.HATTON, JRNL AUTH 2 S.KLEINE-DOPKE,A.BERKES,G.GORE,J.P.LEIMKOHL,H.SCHIKORA, JRNL AUTH 3 M.KOLLEWE,H.ROHDE,M.WILMANNS,F.TELLKAMP,E.C.SCHULZ JRNL TITL MILLISECOND CRYO-TRAPPING BY THE SPITROBOT CRYSTAL PLUNGER JRNL TITL 2 SIMPLIFIES TIME-RESOLVED CRYSTALLOGRAPHY. JRNL REF NAT COMMUN V. 14 2365 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 37185266 JRNL DOI 10.1038/S41467-023-37834-W REMARK 2 REMARK 2 RESOLUTION. 1.78 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.78 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.81 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 57.0 REMARK 3 NUMBER OF REFLECTIONS : 13530 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.140 REMARK 3 FREE R VALUE TEST SET COUNT : 696 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 38.8100 - 3.0500 0.92 4388 222 0.1879 0.2415 REMARK 3 2 3.0500 - 2.4200 0.91 4072 251 0.2452 0.2890 REMARK 3 3 2.4200 - 2.1200 0.76 3394 177 0.2777 0.3232 REMARK 3 4 2.1100 - 1.9600 0.25 860 43 0.2974 0.2968 REMARK 3 5 1.8600 - 1.7800 0.04 120 3 0.3267 0.5524 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.208 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.415 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.23 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.12 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 : 0.003 2026 REMARK 3 ANGLE : 0.657 2768 REMARK 3 CHIRALITY : 0.042 328 REMARK 3 PLANARITY : 0.006 365 REMARK 3 DIHEDRAL : 5.045 293 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 5.7649 -1.2623 19.7023 REMARK 3 T TENSOR REMARK 3 T11: 0.1851 T22: 0.0369 REMARK 3 T33: 0.0877 T12: 0.0859 REMARK 3 T13: 0.0082 T23: -0.0241 REMARK 3 L TENSOR REMARK 3 L11: 0.3265 L22: 1.1128 REMARK 3 L33: 3.3732 L12: 0.1748 REMARK 3 L13: -0.1199 L23: -1.0774 REMARK 3 S TENSOR REMARK 3 S11: 0.0692 S12: 0.0354 S13: -0.0930 REMARK 3 S21: -0.1931 S22: -0.0703 S23: -0.0103 REMARK 3 S31: 0.6422 S32: 0.3772 S33: 0.0209 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 8B2W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-SEP-22. REMARK 100 THE DEPOSITION ID IS D_1292125636. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-FEB-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P14 (MX2) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97626 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13533 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.780 REMARK 200 RESOLUTION RANGE LOW (A) : 77.621 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 79.9 REMARK 200 DATA REDUNDANCY : 10.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.78 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.08 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: 6GTH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40% PEG8000, 200 MM LISO4, 100 MM REMARK 280 NAOAC, PH 4.5, BATCH MODE, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 155.24267 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 77.62133 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 77.62133 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 155.24267 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 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 GLN A 32 CG CD OE1 NE2 REMARK 480 LYS A 39 CD CE NZ REMARK 480 GLN A 89 CG CD OE1 NE2 REMARK 480 LYS A 98 CD CE NZ REMARK 480 GLU A 271 CG CD OE1 OE2 REMARK 480 GLU A 286 CD 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 -133.70 56.23 REMARK 500 GLN A 89 40.68 -101.42 REMARK 500 VAL A 103 -143.51 -127.45 REMARK 500 SER A 220 -123.69 -102.65 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 568 DISTANCE = 6.07 ANGSTROMS REMARK 525 HOH A 569 DISTANCE = 6.23 ANGSTROMS DBREF 8B2W A 28 287 UNP D2D9A0 D2D9A0_KLEPN 23 282 SEQADV 8B2W ALA A 166 UNP D2D9A0 GLU 161 ENGINEERED MUTATION SEQRES 1 A 260 SER ALA VAL GLN GLN LYS LEU ALA ALA LEU GLU LYS SER SEQRES 2 A 260 SER GLY GLY ARG LEU GLY VAL ALA LEU ILE ASP THR ALA SEQRES 3 A 260 ASP ASN THR GLN VAL LEU TYR ARG GLY ASP GLU ARG PHE SEQRES 4 A 260 PRO MET CYS SER THR SER LYS VAL MET ALA ALA ALA ALA SEQRES 5 A 260 VAL LEU LYS GLN SER GLU THR GLN LYS GLN LEU LEU ASN SEQRES 6 A 260 GLN PRO VAL GLU ILE LYS PRO ALA ASP LEU VAL ASN TYR SEQRES 7 A 260 ASN PRO ILE ALA GLU LYS HIS VAL ASN GLY THR MET THR SEQRES 8 A 260 LEU ALA GLU LEU SER ALA ALA ALA LEU GLN TYR SER ASP SEQRES 9 A 260 ASN THR ALA MET ASN LYS LEU ILE ALA GLN LEU GLY GLY SEQRES 10 A 260 PRO GLY GLY VAL THR ALA PHE ALA ARG ALA ILE GLY ASP SEQRES 11 A 260 GLU THR PHE ARG LEU ASP ARG THR ALA PRO THR LEU ASN SEQRES 12 A 260 THR ALA ILE PRO GLY ASP PRO ARG ASP THR THR THR PRO SEQRES 13 A 260 ARG ALA MET ALA GLN THR LEU ARG GLN LEU THR LEU GLY SEQRES 14 A 260 HIS ALA LEU GLY GLU THR GLN ARG ALA GLN LEU VAL THR SEQRES 15 A 260 TRP LEU LYS GLY ASN THR THR GLY ALA ALA SER ILE ARG SEQRES 16 A 260 ALA GLY LEU PRO THR SER TRP THR VAL GLY ASP LYS THR SEQRES 17 A 260 GLY SER GLY ASP TYR GLY THR THR ASN ASP ILE ALA VAL SEQRES 18 A 260 ILE TRP PRO GLN GLY ARG ALA PRO LEU VAL LEU VAL THR SEQRES 19 A 260 TYR PHE THR GLN PRO GLN GLN ASN ALA GLU SER ARG ARG SEQRES 20 A 260 ASP VAL LEU ALA SER ALA ALA ARG ILE ILE ALA GLU GLY HET AIX A 301 24 HETNAM AIX (2R,4S)-2-[(1R)-1-{[(2R)-2-AMINO-2-PHENYLACETYL]AMINO}- HETNAM 2 AIX 2-OXOETHYL]-5,5-DIMETHYL-1,3-THIAZOLIDINE-4-CARBOXYLIC HETNAM 3 AIX ACID HETSYN AIX AMPICILLIN (OPEN FORM) FORMUL 2 AIX C16 H21 N3 O4 S FORMUL 3 HOH *169(H2 O) HELIX 1 AA1 SER A 28 GLY A 42 1 15 HELIX 2 AA2 CYS A 69 THR A 71 5 3 HELIX 3 AA3 SER A 72 SER A 84 1 13 HELIX 4 AA4 LYS A 98 LEU A 102 5 5 HELIX 5 AA5 ILE A 108 VAL A 113 5 6 HELIX 6 AA6 LEU A 119 TYR A 129 1 11 HELIX 7 AA7 ASP A 131 LEU A 142 1 12 HELIX 8 AA8 GLY A 144 ILE A 155 1 12 HELIX 9 AA9 PRO A 167 THR A 171 5 5 HELIX 10 AB1 THR A 182 LEU A 195 1 14 HELIX 11 AB2 GLY A 200 GLY A 213 1 14 HELIX 12 AB3 SER A 220 LEU A 225 5 6 HELIX 13 AB4 ARG A 273 GLU A 286 1 14 SHEET 1 AA1 5 THR A 56 TYR A 60 0 SHEET 2 AA1 5 ARG A 44 ASP A 51 -1 N ASP A 51 O THR A 56 SHEET 3 AA1 5 LEU A 257 THR A 264 -1 O TYR A 262 N GLY A 46 SHEET 4 AA1 5 THR A 243 TRP A 250 -1 N ILE A 249 O LEU A 257 SHEET 5 AA1 5 THR A 230 SER A 237 -1 N GLY A 236 O ASN A 244 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 LINK OG SER A 70 C15 AIX A 301 1555 1555 1.41 CISPEP 1 ALA A 166 PRO A 167 0 4.32 CRYST1 41.812 41.812 232.864 90.00 90.00 120.00 P 32 2 1 6 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 0.023917 0.013808 0.000000 0.00000 SCALE2 0.000000 0.027616 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004294 0.00000