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- PDB-2qpn: GES-1 beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 2qpn
TitleGES-1 beta-lactamase
ComponentsBeta-lactamase GES-1
KeywordsHYDROLASE / beta-lactamase / apo-enzyme / Plasmid
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Beta-lactamase GES-1
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsSmith, C.A. / Caccamo, M. / Kantardjieff, K.A. / Vakulenko, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Structure of GES-1 at atomic resolution: insights into the evolution of carbapenamase activity in the class A extended-spectrum beta-lactamases.
Authors: Smith, C.A. / Caccamo, M. / Kantardjieff, K.A. / Vakulenko, S.
History
DepositionJul 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase GES-1
B: Beta-lactamase GES-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5774
Polymers62,3852
Non-polymers1922
Water13,115728
1
A: Beta-lactamase GES-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2892
Polymers31,1921
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase GES-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2892
Polymers31,1921
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.410, 80.820, 71.440
Angle α, β, γ (deg.)90.00, 101.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase GES-1 / GES-1 extended-spectrum beta-lactamase


Mass: 31192.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: ges-1, blaGES-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KJY7
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 728 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.92 Å3/Da / Density % sol: 36.06 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 10% PEG8000, 10% PEG1000, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.82653 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 23, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82653 Å / Relative weight: 1
ReflectionResolution: 1→20 Å / Num. all: 237028 / Num. obs: 163829 / % possible obs: 93.4 % / Observed criterion σ(F): 4 / Rmerge(I) obs: 0.046 / Net I/σ(I): 11.47
Reflection shellResolution: 1→1.05 Å / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 2.69 / % possible all: 90.1

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Processing

Software
NameVersionClassification
Blu-Ice5data collection
MOLREPphasing
SHELXL-97refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: anisotropic displacement parameter refinement
RfactorNum. reflectionSelection details
Rfree0.1821 9025 5% randomly selected
Rwork0.133 --
all0.1354 179807 -
obs-163829 -
Displacement parametersBiso mean: 18 Å2
Refinement stepCycle: LAST / Resolution: 1.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4135 0 10 728 4873
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.072
X-RAY DIFFRACTIONs_zero_chiral_vol0.082
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.098
X-RAY DIFFRACTIONs_approx_iso_adps0.092

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