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- PDB-1gce: STRUCTURE OF THE BETA-LACTAMASE OF ENTEROBACTER CLOACAE GC1 -

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Basic information

Entry
Database: PDB / ID: 1gce
TitleSTRUCTURE OF THE BETA-LACTAMASE OF ENTEROBACTER CLOACAE GC1
ComponentsBETA-LACTAMASE
KeywordsHYDROLASE / BETA-LACTAM HYDROLASE / CEPHALOSPORINASE / DRUG DESIGN / EXTENDED-SPECTRUM BETA- LACTAMASE
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCrichlow, G.V. / Kuzin, A.P. / Nukaga, M. / Sawai, T. / Knox, J.R.
CitationJournal: Biochemistry / Year: 1999
Title: Structure of the extended-spectrum class C beta-lactamase of Enterobacter cloacae GC1, a natural mutant with a tandem tripeptide insertion.
Authors: Crichlow, G.V. / Kuzin, A.P. / Nukaga, M. / Mayama, K. / Sawai, T. / Knox, J.R.
History
DepositionMay 17, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 27, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-LACTAMASE


Theoretical massNumber of molelcules
Total (without water)39,6091
Polymers39,6091
Non-polymers00
Water4,234235
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.975, 69.514, 63.142
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-512-

HOH

21A-538-

HOH

31A-625-

HOH

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Components

#1: Protein BETA-LACTAMASE / / CEPHALOSPORINASE


Mass: 39609.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Strain: GC1 / Cellular location: PERIPLASM / Plasmid: PTTQ18K-GC1 / Gene (production host): BLAC / Production host: Escherichia coli (E. coli) / Strain (production host): AS226-51 / References: UniProt: P05364, beta-lactamase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43 %
Description: PH GIVEN IS THAT OF A SOLUTION SIMILAR TO THE RESERVOIR SOLUION. THE PH FALLS IN THE RANGE OF 4 - 6.
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5
Details: VAPOR DIFFUSION, WITH 6.7 OR 8.0 MG/ML PROTEIN IN 5-7.5% PEG8000, 20-25MM POTASSIUM PHOSPHATE (MONOBASIC), OVER 12.5 OR 15% PEG8000, 50MM POTASSIUM PHOSPHATE (MONOBASIC) RESERVOIR AT ROOM ...Details: VAPOR DIFFUSION, WITH 6.7 OR 8.0 MG/ML PROTEIN IN 5-7.5% PEG8000, 20-25MM POTASSIUM PHOSPHATE (MONOBASIC), OVER 12.5 OR 15% PEG8000, 50MM POTASSIUM PHOSPHATE (MONOBASIC) RESERVOIR AT ROOM TEMPERATURE., temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
113.4 mg/mlprotein1drop
212.5-15 %PEG80001reservoir
30.05-0.1 M1reservoirKH2PO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908
DetectorType: ADSC / Detector: CCD / Date: Aug 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 1.8→99 Å / Num. obs: 31187 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 11.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.79 % / Rmerge(I) obs: 0.142 / Mean I/σ(I) obs: 5 / Rsym value: 0.142 / % possible all: 80
Reflection
*PLUS
% possible obs: 96 % / Num. measured all: 122470
Reflection shell
*PLUS
% possible obs: 80 % / Num. unique obs: 2568 / Num. measured obs: 4591 / Mean I/σ(I) obs: 5.1

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BLT

2blt
PDB Unreleased entry


Resolution: 1.8→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
Details: AFTER FINAL REFINEMENT, ONE WATER MOLECULE WAS DELETED FROM MODEL DUE TO B- FACTOR MORE THAN 55. AVG. B GIVEN REFLECTS STRUCTURE INCLUDING PROTEIN AND ONLY 235 WATER MOLECULES. THE FINAL ...Details: AFTER FINAL REFINEMENT, ONE WATER MOLECULE WAS DELETED FROM MODEL DUE TO B- FACTOR MORE THAN 55. AVG. B GIVEN REFLECTS STRUCTURE INCLUDING PROTEIN AND ONLY 235 WATER MOLECULES. THE FINAL ELECTRON DENSITY MAP CLEARLY SHOWS THAT NZ OF LYS67 IS COVALENTLY CROSSLINKED TO CE1 OF TYR150 VIA A BRIDGING (UNMODELED) ATOM, POSSIBLY NITROGEN. THIS UNUSUAL LINKAGE MIGHT HAVE DERIVED FROM THE AZIDE PRESENT IN THE LOW PH BUFFER.
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1502 5 %RANDOM
Rwork0.2018 ---
obs-30206 94.2 %-
Displacement parametersBiso mean: 15.1 Å2
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2773 0 0 235 3008
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.405
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.249
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.8→1.88 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2626 190 6 %
Rwork0.2482 2965 -
obs--79.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PROTEIN_REP.PARAMTOPH19.SOL
X-RAY DIFFRACTION3PARAM19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.23 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.249

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