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- PDB-3ni9: GES-2 carbapenemase apo form -

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Basic information

Entry
Database: PDB / ID: 3ni9
TitleGES-2 carbapenemase apo form
ComponentsBeta-lactamase GES-2
KeywordsHYDROLASE / beta-lactamase / antibiotic resistance / carbapenemase
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / 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-2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFrase, H. / Smith, C.A. / Toth, M. / Vakulenko, S.B.
CitationJournal: Biochemistry / Year: 2015
Title: Kinetic and structural requirements for carbapenemase activity in GES-type beta-lactamases.
Authors: Stewart, N.K. / Smith, C.A. / Frase, H. / Black, D.J. / Vakulenko, S.B.
History
DepositionJun 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 21, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase GES-2
B: Beta-lactamase GES-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0954
Polymers58,6182
Non-polymers4772
Water6,197344
1
A: Beta-lactamase GES-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5472
Polymers29,3091
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase GES-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5472
Polymers29,3091
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.460, 80.540, 87.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase GES-2 / Expanded-spectrum beta-lactamase GES-2


Mass: 29309.160 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 19-287
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: bla GES-2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q93F76
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 2.31 Å3/Da / Density % sol: 46.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.8
Details: 0.02 M citric acid, 0.08 M Bis-Tris propane, pH 8.8, 16% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9785 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 30, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2→29.7 Å / Num. all: 36138 / Num. obs: 36138 / % possible obs: 94.7 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 12.1
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 2.72 / % possible all: 99.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
PHENIX(phenix.refine: 1.6_289)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QPN

2qpn


Resolution: 2→29.69 Å / SU ML: 0.33 / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2791 1759 5.02 %
Rwork0.2185 --
obs0.2215 35064 93.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.494 Å2 / ksol: 0.316 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.2997 Å2-0 Å20 Å2
2---5.1639 Å20 Å2
3---10.4636 Å2
Refinement stepCycle: LAST / Resolution: 2→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4092 0 30 344 4466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084200
X-RAY DIFFRACTIONf_angle_d1.095682
X-RAY DIFFRACTIONf_dihedral_angle_d17.631554
X-RAY DIFFRACTIONf_chiral_restr0.072648
X-RAY DIFFRACTIONf_plane_restr0.005738
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05410.2931490.23712688X-RAY DIFFRACTION100
2.0541-2.11450.35881390.25182669X-RAY DIFFRACTION100
2.1145-2.18270.28981330.24562697X-RAY DIFFRACTION100
2.1827-2.26070.3905590.30461254X-RAY DIFFRACTION52
2.2607-2.35120.31981100.25242415X-RAY DIFFRACTION93
2.3512-2.45810.30171480.22342703X-RAY DIFFRACTION100
2.4581-2.58770.281520.20822713X-RAY DIFFRACTION100
2.5877-2.74970.30591480.20272689X-RAY DIFFRACTION100
2.7497-2.96180.27691440.2052716X-RAY DIFFRACTION100
2.9618-3.25950.26381540.21062725X-RAY DIFFRACTION100
3.2595-3.73040.30961320.26162439X-RAY DIFFRACTION89
3.7304-4.69690.24091500.18292680X-RAY DIFFRACTION97
4.6969-29.69280.21171410.16762917X-RAY DIFFRACTION100

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