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- PDB-4zdx: Structure of OXA-51 beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 4zdx
TitleStructure of OXA-51 beta-lactamase
ComponentsBeta-lactamase
KeywordsHYDROLASE / antibiotic resistance / beta-lactamase / carbapenemase / mutant
Function / homology
Function and homology information


Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL / Beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsSmith, C.A. / Antunes, N.T. / Stewart, N.K. / Frase, H. / Toth, M. / Kantardjieff, K.A. / Vakulenko, S.B.
CitationJournal: Acs Chem.Biol. / Year: 2015
Title: Structural Basis for Enhancement of Carbapenemase Activity in the OXA-51 Family of Class D beta-Lactamases.
Authors: Smith, C.A. / Antunes, N.T. / Stewart, N.K. / Frase, H. / Toth, M. / Kantardjieff, K.A. / Vakulenko, S.
History
DepositionApr 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2Apr 2, 2025Group: 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9583
Polymers30,7021
Non-polymers2562
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)131.111, 131.111, 67.525
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-527-

HOH

21A-543-

HOH

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Components

#1: Protein Beta-lactamase / Beta-lactamase OXA-51


Mass: 30702.104 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5QT35
#2: Chemical ChemComp-TOE / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL


Mass: 164.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16O4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.35 Å3/Da / Density % sol: 47.95 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M magnesium chloride hexahydrate, 0.1 M HEPES sodium, pH 7.5, 30% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→33.8 Å / Num. all: 20085 / Num. obs: 20085 / % possible obs: 99.7 % / Redundancy: 6.4 % / Rsym value: 0.043 / Net I/σ(I): 26.4
Reflection shellResolution: 2→2.05 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.5 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.001→33.763 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2161 1028 5.12 %
Rwork0.1566 --
obs0.1595 20084 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.001→33.763 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1908 0 17 145 2070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071971
X-RAY DIFFRACTIONf_angle_d1.0152664
X-RAY DIFFRACTIONf_dihedral_angle_d14.597734
X-RAY DIFFRACTIONf_chiral_restr0.043291
X-RAY DIFFRACTIONf_plane_restr0.006340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.001-2.10650.26051490.20892669X-RAY DIFFRACTION99
2.1065-2.23840.24181490.17582679X-RAY DIFFRACTION100
2.2384-2.41120.20921340.17252708X-RAY DIFFRACTION100
2.4112-2.65380.23891700.1692661X-RAY DIFFRACTION100
2.6538-3.03760.23081510.17192713X-RAY DIFFRACTION100
3.0376-3.82620.23291450.15212744X-RAY DIFFRACTION100
3.8262-33.76730.17841300.14012882X-RAY DIFFRACTION99
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)
10.1988-0.11310.25190.2997-0.0170.3570.6856-0.00680.4867-0.3513-0.46740.1398-1.0444-1.09580.01870.77010.0227-0.09980.82730.24590.7613-0.153151.559412.3953
21.65450.1766-0.36810.75650.11640.92270.06590.35190.0734-0.21770.05190.193-0.0453-0.3363-0.00010.3074-0.0044-0.06360.43830.0380.34673.902634.017816.965
31.23070.28310.75060.7690.27141.04210.00220.22340.0922-0.17940.0449-0.1-0.02280.43280.00020.35920.00030.01810.4397-0.00110.398126.632426.109218.5626
40.4935-0.60710.35490.9438-0.0640.9192-0.11470.2438-0.4514-0.43880.1335-0.02420.4415-0.05390.00020.4063-0.049-0.01790.3199-0.05830.426714.100717.038319.0341
51.4613-0.17220.42161.4232-0.3740.7943-0.03280.2627-0.1113-0.26670.09040.24370.1697-0.33940.00010.3043-0.069-0.0550.383-0.02250.35016.165224.856118.8067
60.72870.16340.04860.3503-0.45630.61970.1406-0.28650.30540.4026-0.07890.3676-0.11240.33430.00050.3002-0.0151-0.01750.4044-0.02640.348215.568633.50330.5544
72.2456-0.2390.53961.9804-0.93460.83430.03810.30050.2488-0.2530.06120.0696-0.1865-0.07410.00440.2809-0.051-0.0030.36470.03690.32669.911838.710517.1683
80.30010.30030.14620.3303-0.00190.28960.1805-0.04180.4411-0.1850.1024-0.135-0.55860.15440.00070.4241-0.01880.01550.40660.0570.51989.07647.57418.4154
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 34 through 48 )
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 92 )
3X-RAY DIFFRACTION3chain 'A' and (resid 93 through 128 )
4X-RAY DIFFRACTION4chain 'A' and (resid 129 through 151 )
5X-RAY DIFFRACTION5chain 'A' and (resid 152 through 193 )
6X-RAY DIFFRACTION6chain 'A' and (resid 194 through 209 )
7X-RAY DIFFRACTION7chain 'A' and (resid 210 through 256 )
8X-RAY DIFFRACTION8chain 'A' and (resid 257 through 274 )

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