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- PDB-9env: Apo GES-1 beta-Lactamase Crystallised with Citric Acid -

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Basic information

Entry
Database: PDB / ID: 9env
TitleApo GES-1 beta-Lactamase Crystallised with Citric Acid
Componentsbeta-lactamase
KeywordsANTIMICROBIAL PROTEIN / beta-lactamase / antibiotic resistance / enzyme / apo
Function / homologyBeta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / beta-lactam antibiotic catabolic process / Beta-lactamase, class-A / Beta-lactamase/transpeptidase-like / beta-lactamase activity / beta-lactamase / response to antibiotic / Beta-lactamase GES-1
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBeer, M. / Hinchliffe, P. / Spencer, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T008741/10 United Kingdom
CitationJournal: To Be Published
Title: Apo GES-1 beta-Lactamase Crystallised with Citric Acid
Authors: Beer, M. / Hinchliffe, P. / Spencer, J.
History
DepositionMar 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: beta-lactamase
B: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4164
Polymers62,9392
Non-polymers4772
Water11,277626
1
A: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7082
Polymers31,4701
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7082
Polymers31,4701
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.564, 80.814, 104.543
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein beta-lactamase


Mass: 31469.564 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, beta-lactamase
#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.: 626 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 8.8
Details: 0.02 M citric acid, 0.08 M Bis-Tris propane, 10 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.7838 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 3, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7838 Å / Relative weight: 1
ReflectionResolution: 1.6→43.91 Å / Num. obs: 85097 / % possible obs: 100 % / Redundancy: 14 % / Biso Wilson estimate: 22.62 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.064 / Net I/σ(I): 6.9
Reflection shellResolution: 1.6→1.63 Å / Mean I/σ(I) obs: 0.4 / Num. unique obs: 4160 / CC1/2: 0.324 / Rpim(I) all: 1.083

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→43.89 Å / SU ML: 0.2523 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.4269
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2091 1991 2.35 %
Rwork0.1791 82872 -
obs0.1798 84863 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.39 Å2
Refinement stepCycle: LAST / Resolution: 1.6→43.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4086 0 30 626 4742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01064192
X-RAY DIFFRACTIONf_angle_d1.06425673
X-RAY DIFFRACTIONf_chiral_restr0.0596648
X-RAY DIFFRACTIONf_plane_restr0.0104735
X-RAY DIFFRACTIONf_dihedral_angle_d14.23381559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.39251460.40325697X-RAY DIFFRACTION97.56
1.64-1.680.41111220.36555883X-RAY DIFFRACTION99.7
1.68-1.730.32861470.32385830X-RAY DIFFRACTION99.8
1.73-1.790.28761620.28695849X-RAY DIFFRACTION99.92
1.79-1.850.27991450.25245870X-RAY DIFFRACTION99.9
1.85-1.930.26191590.23345884X-RAY DIFFRACTION99.95
1.93-2.020.23091400.20845878X-RAY DIFFRACTION99.97
2.02-2.120.22651260.16985896X-RAY DIFFRACTION99.95
2.12-2.250.19551160.15795957X-RAY DIFFRACTION99.98
2.25-2.430.19421340.15125925X-RAY DIFFRACTION100
2.43-2.670.18941480.15235946X-RAY DIFFRACTION99.95
2.67-3.060.19521390.15745979X-RAY DIFFRACTION99.97
3.06-3.850.16481610.14986019X-RAY DIFFRACTION100
3.85-43.890.19281460.15726259X-RAY DIFFRACTION99.92

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