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- PDB-3v3s: Crystal structure of GES-18 -

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Basic information

Entry
Database: PDB / ID: 3v3s
TitleCrystal structure of GES-18
ComponentsExtended spectrum beta-lactamase GES-18
KeywordsHYDROLASE / Beta lactamase fold / Beta Lactams
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
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDelbruck, H. / Hoffmann, K.M.V. / Bebrone, C.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2013
Title: GES-18, a new carbapenem-hydrolyzing GES-Type beta-lactamase from pseudomonas aeruginosa that contains Ile80 and Ser170 residues.
Authors: Bebrone, C. / Bogaerts, P. / Delbruck, H. / Bennink, S. / Kupper, M.B. / Rezende de Castro, R. / Glupczynski, Y. / Hoffmann, K.M.
History
DepositionDec 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Sep 13, 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
Revision 1.3Nov 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: Extended spectrum beta-lactamase GES-18
B: Extended spectrum beta-lactamase GES-18


Theoretical massNumber of molelcules
Total (without water)62,4732
Polymers62,4732
Non-polymers00
Water7,927440
1
A: Extended spectrum beta-lactamase GES-18


Theoretical massNumber of molelcules
Total (without water)31,2361
Polymers31,2361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Extended spectrum beta-lactamase GES-18


Theoretical massNumber of molelcules
Total (without water)31,2361
Polymers31,2361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.184, 80.506, 87.748
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 Extended spectrum beta-lactamase GES-18 / GES-5 / GES-5 extended-spectrum beta-lactamase / Metallo-beta-lactamase blaGES-5


Mass: 31236.492 Da / Num. of mol.: 2 / Fragment: BETA-LACTAMASE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: pa41437 / Gene: blaGes / Plasmid: pET28-GES18 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: H2ERK4*PLUS, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 2.15 Å3/Da / Density % sol: 42.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.8
Details: 0.02 M citric acid, 0.08 M Bis-Tris propane, 10 % PEG 3350 , pH 8.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 21, 2011 / Details: mirror
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.87→25 Å / Num. all: 43240 / Num. obs: 43240 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 18.1 Å2 / Rsym value: 0.046 / Net I/σ(I): 24.8
Reflection shellResolution: 1.87→1.97 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 5.9 / Num. unique all: 5966 / Rsym value: 0.267 / % possible all: 90.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.6.0119refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QPN

2qpn


Resolution: 1.9→25 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19555 2097 5 %RANDOM
Rwork0.1576 ---
all0.15952 41653 --
obs0.15952 39556 96.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.827 Å2
Baniso -1Baniso -2Baniso -3
1--1.7 Å20 Å20 Å2
2---1.78 Å20 Å2
3---3.48 Å2
Refinement stepCycle: LAST / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4095 0 0 440 4535
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194399
X-RAY DIFFRACTIONr_bond_other_d00.023065
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.9625988
X-RAY DIFFRACTIONr_angle_other_deg4.1643.0017460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7215593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.42123.147197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.31215787
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4581546
X-RAY DIFFRACTIONr_chiral_restr0.1010.2682
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024988
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02926
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 142 -
Rwork0.186 2818 -
obs-2960 93.73 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.82940.44330.01891.6523-0.17030.43120.0868-0.05080.01030.1699-0.13960.18030.0407-0.02980.05290.1578-0.04110.02530.208-0.02170.0355-30.6-30.83724.315
20.54110.2848-0.06241.4255-0.40820.3744-0.01540.02540.04680.0060.06910.0308-0.0145-0.0484-0.05380.14730.00290.00940.1890.00470.0131-8.563-6.05215.13
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 287
2X-RAY DIFFRACTION2B19 - 286

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