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- PDB-4z9q: Crystal structure of OXA-58 with disordered active site -

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Basic information

Entry
Database: PDB / ID: 4z9q
TitleCrystal structure of OXA-58 with disordered active site
ComponentsBeta-lactamase OXA-58
KeywordsHYDROLASE / OXA-58 / Beta lactamase / Disordered / BALBES NMR
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase / beta-lactamase activity / response to antibiotic / plasma membrane
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / : / 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
Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii ACICU (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.23 Å
AuthorsPratap, S. / Gill, P.K. / Golemi-Kotra, D. / Kumar, P.
CitationJournal: To Be Published
Title: Crystal structure of OXA-58 with disordered active site
Authors: Pratap, S. / Gill, P.K. / Golemi-Kotra, D. / Kumar, P.
History
DepositionApr 11, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 9, 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

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Assembly

Deposited unit
A: Beta-lactamase OXA-58


Theoretical massNumber of molelcules
Total (without water)31,4981
Polymers31,4981
Non-polymers00
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10350 Å2
Unit cell
Length a, b, c (Å)37.360, 39.790, 72.090
Angle α, β, γ (deg.)90.00, 91.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase OXA-58


Mass: 31498.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii ACICU (bacteria)
Strain: ACICU / Plasmid: pET29a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: B2I3T3, UniProt: A0A182DW26*PLUS, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 1.7008 Å3/Da / Density % sol: 27.6791 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.23→37.38 Å / Num. obs: 10289 / % possible obs: 98.28 % / Redundancy: 2 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 16.39
Reflection shellResolution: 2.235→2.314 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 5.84 / % possible all: 93.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
SCALAdata reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 2.23→37.38 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.895 / SU B: 16.609 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.387 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25259 500 4.9 %RANDOM
Rwork0.19218 ---
obs0.1951 9789 98.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.573 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20.33 Å2
2---0.59 Å20 Å2
3---0.65 Å2
Refinement stepCycle: 1 / Resolution: 2.23→37.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1789 0 0 62 1851
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191826
X-RAY DIFFRACTIONr_bond_other_d0.0020.021764
X-RAY DIFFRACTIONr_angle_refined_deg1.3151.9532466
X-RAY DIFFRACTIONr_angle_other_deg0.934048
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6065221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.02724.82887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.06815316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.579159
X-RAY DIFFRACTIONr_chiral_restr0.0730.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022066
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02427
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_it0.3921.914893
X-RAY DIFFRACTIONr_mcbond_other0.3921.913892
X-RAY DIFFRACTIONr_mcangle_it0.7432.8651111
X-RAY DIFFRACTIONr_mcangle_other0.7432.8671112
X-RAY DIFFRACTIONr_scbond_it0.1721.936933
X-RAY DIFFRACTIONr_scbond_other0.1721.937934
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.3772.8951356
X-RAY DIFFRACTIONr_long_range_B_refined2.76815.3122069
X-RAY DIFFRACTIONr_long_range_B_other2.75515.2832064
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.235→2.292 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.453 32 -
Rwork0.321 653 -
obs--91.09 %
Refinement TLS params.Method: refined / Origin x: 10.483 Å / Origin y: 2.474 Å / Origin z: 16.124 Å
111213212223313233
T0.0101 Å20.0051 Å20.0044 Å2-0.1073 Å20.0259 Å2--0.0293 Å2
L2.9076 °20.7625 °20.7099 °2-2.0299 °20.8179 °2--3.1966 °2
S0.0245 Å °-0.301 Å °-0.0166 Å °0.001 Å °0.0216 Å °-0.0979 Å °-0.1492 Å °0.0012 Å °-0.0461 Å °

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