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- PDB-4gnu: Crystal structure of GES-5 carbapenemase -

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Basic information

Entry
Database: PDB / ID: 4gnu
TitleCrystal structure of GES-5 carbapenemase
ComponentsBeta-lactamase GES-5
KeywordsHYDROLASE / beta-lactamase / carbapenemase
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
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å
AuthorsSmith, C.A. / Vakulenko, S.B.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: Structural basis for progression toward the carbapenemase activity in the GES family of beta-lactamases.
Authors: Smith, C.A. / Frase, H. / Toth, M. / Kumarasiri, M. / Wiafe, K. / Munoz, J. / Mobashery, S. / Vakulenko, S.B.
History
DepositionAug 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 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-5
B: Beta-lactamase GES-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9224
Polymers62,4452
Non-polymers4772
Water10,503583
1
A: Beta-lactamase GES-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4612
Polymers31,2221
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase GES-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4612
Polymers31,2221
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.660, 80.470, 71.230
Angle α, β, γ (deg.)90.00, 101.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase GES-5 / Extended spectrum beta-lactamase GES-5 / Extended-spectrum beta-lactamase GES-5 / GES-5 / GES-5 ...Extended spectrum beta-lactamase GES-5 / Extended-spectrum beta-lactamase GES-5 / GES-5 / GES-5 extended-spectrum beta-lactamase / Metallo-beta-lactamase blaGES-5


Mass: 31222.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaGES-5 / Production host: Escherichia coli (E. coli) / References: UniProt: A0EL75
#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.: 583 / 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: 35.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: unbuffered 0.2% sodium iodide and 18-20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.82654 Å
DetectorType: RAYONIX MX-325 / Detector: CCD / Date: Jun 25, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82654 Å / Relative weight: 1
ReflectionResolution: 1.086→32 Å / Num. all: 191963 / Num. obs: 191963 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.6
Reflection shellResolution: 1.09→1.11 Å / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 2.11 / % possible all: 87.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.09→32.02 Å / SU ML: 0.14 / σ(F): 1.36 / Phase error: 15.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1716 9538 5 %random 5%
Rwork0.1563 ---
obs0.1571 190745 97.44 %-
all-190745 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.166 Å2 / ksol: 0.405 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.9365 Å2-0 Å2-2.3386 Å2
2--0.1698 Å2-0 Å2
3----1.1062 Å2
Refinement stepCycle: LAST / Resolution: 1.09→32.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4044 0 30 583 4657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064369
X-RAY DIFFRACTIONf_angle_d1.1475964
X-RAY DIFFRACTIONf_dihedral_angle_d14.1851704
X-RAY DIFFRACTIONf_chiral_restr0.078684
X-RAY DIFFRACTIONf_plane_restr0.006777
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.09-1.10240.26233030.25255835X-RAY DIFFRACTION94
1.1024-1.11540.26393120.23255939X-RAY DIFFRACTION96
1.1154-1.1290.24433140.21815957X-RAY DIFFRACTION96
1.129-1.14330.22193120.20925906X-RAY DIFFRACTION96
1.1433-1.15830.19793140.19085950X-RAY DIFFRACTION96
1.1583-1.17420.21193120.18685975X-RAY DIFFRACTION96
1.1742-1.19090.19893140.18445938X-RAY DIFFRACTION97
1.1909-1.20870.20653170.18296008X-RAY DIFFRACTION97
1.2087-1.22760.20143140.17975968X-RAY DIFFRACTION97
1.2276-1.24770.19283180.17066047X-RAY DIFFRACTION97
1.2477-1.26920.18943140.17355964X-RAY DIFFRACTION97
1.2692-1.29230.18523140.15985999X-RAY DIFFRACTION97
1.2923-1.31720.17513180.15696016X-RAY DIFFRACTION97
1.3172-1.34410.17183190.15266050X-RAY DIFFRACTION97
1.3441-1.37330.17843160.14515980X-RAY DIFFRACTION97
1.3733-1.40520.16953190.13986014X-RAY DIFFRACTION98
1.4052-1.44040.16843150.13546055X-RAY DIFFRACTION98
1.4404-1.47930.14113200.13116082X-RAY DIFFRACTION98
1.4793-1.52290.15133200.12636051X-RAY DIFFRACTION98
1.5229-1.5720.16233230.1256078X-RAY DIFFRACTION98
1.572-1.62820.15593190.12666055X-RAY DIFFRACTION98
1.6282-1.69340.15643210.13046080X-RAY DIFFRACTION98
1.6934-1.77040.15793200.1386119X-RAY DIFFRACTION99
1.7704-1.86380.1573210.14396144X-RAY DIFFRACTION99
1.8638-1.98050.16173250.15136162X-RAY DIFFRACTION99
1.9805-2.13340.16753270.15396186X-RAY DIFFRACTION99
2.1334-2.34810.17153220.14956132X-RAY DIFFRACTION99
2.3481-2.68770.17013270.15836198X-RAY DIFFRACTION99
2.6877-3.38560.16063240.16156174X-RAY DIFFRACTION99
3.3856-32.03380.17273240.16336145X-RAY DIFFRACTION97

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