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- PDB-5iy2: Structure of apo OXA-143 carbapenemase -

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Basic information

Entry
Database: PDB / ID: 5iy2
TitleStructure of apo OXA-143 carbapenemase
ComponentsBeta-lactamase OXA-143
KeywordsHYDROLASE / Antibiotic resistance / carbapenemase / enzyme kinetics / mechanism of resistance
Function / homologyPenicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / penicillin binding / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta / Beta-lactamase OXA-143
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.15 Å
AuthorsSmith, C.A. / Vakulenko, S.B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI114668 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103393 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: The role of conserved surface hydrophobic residues in the carbapenemase activity of the class D beta-lactamases.
Authors: Toth, M. / Smith, C.A. / Antunes, N.T. / Stewart, N.K. / Maltz, L. / Vakulenko, S.B.
History
DepositionMar 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase OXA-143
B: Beta-lactamase OXA-143
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9414
Polymers54,7572
Non-polymers1842
Water10,449580
1
A: Beta-lactamase OXA-143
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5633
Polymers27,3781
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase OXA-143


Theoretical massNumber of molelcules
Total (without water)27,3781
Polymers27,3781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.955, 62.333, 87.093
Angle α, β, γ (deg.)90.00, 91.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase OXA-143


Mass: 27378.404 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: bla-OXA-143 / Production host: Escherichia coli (E. coli) / References: UniProt: D0UHC8
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 580 / Source method: isolated from a natural source / Formula: H2O

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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: 2.1 Å3/Da / Density % sol: 39.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris-HCl pH 8.5, 0.2 M MgCl2, 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.15→36.625 Å / Num. obs: 150305 / % possible obs: 96.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Net I/σ(I): 11.45
Reflection shellResolution: 1.15→1.18 Å / Redundancy: 3 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 1.9 / % possible all: 87.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.15→36.625 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.27
RfactorNum. reflection% reflectionSelection details
Rfree0.1606 7380 4.91 %random
Rwork0.1362 ---
obs0.1374 150305 96.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: final / Resolution: 1.15→36.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3840 0 12 588 4440
Biso mean--16.48 30.54 -
Num. residues----481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054067
X-RAY DIFFRACTIONf_angle_d0.825510
X-RAY DIFFRACTIONf_dihedral_angle_d15.2331574
X-RAY DIFFRACTIONf_chiral_restr0.081601
X-RAY DIFFRACTIONf_plane_restr0.005704
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.16310.27192030.24544305X-RAY DIFFRACTION87
1.1631-1.17680.262240.22444687X-RAY DIFFRACTION95
1.1768-1.19110.23741980.22164530X-RAY DIFFRACTION93
1.1911-1.20620.24852730.20514692X-RAY DIFFRACTION96
1.2062-1.22210.2042510.1874670X-RAY DIFFRACTION96
1.2221-1.23880.20262630.18014708X-RAY DIFFRACTION96
1.2388-1.25650.19772790.1744676X-RAY DIFFRACTION97
1.2565-1.27530.19292700.17434743X-RAY DIFFRACTION97
1.2753-1.29520.21462250.16324725X-RAY DIFFRACTION97
1.2952-1.31640.18582200.16384831X-RAY DIFFRACTION97
1.3164-1.33910.18662530.15454758X-RAY DIFFRACTION97
1.3391-1.36350.17692380.14654689X-RAY DIFFRACTION96
1.3635-1.38970.18742390.14534658X-RAY DIFFRACTION95
1.3897-1.41810.16412520.12864792X-RAY DIFFRACTION98
1.4181-1.44890.17162320.1254839X-RAY DIFFRACTION98
1.4489-1.48260.16042710.12084787X-RAY DIFFRACTION98
1.4826-1.51970.14642640.11324834X-RAY DIFFRACTION98
1.5197-1.56080.15532340.11374836X-RAY DIFFRACTION98
1.5608-1.60670.13992430.11144809X-RAY DIFFRACTION98
1.6067-1.65860.14292430.10764843X-RAY DIFFRACTION98
1.6586-1.71790.13052480.11394652X-RAY DIFFRACTION95
1.7179-1.78660.14592530.11764856X-RAY DIFFRACTION98
1.7866-1.8680.15212540.11994885X-RAY DIFFRACTION99
1.868-1.96640.15952620.12124864X-RAY DIFFRACTION99
1.9664-2.08960.13012520.11864854X-RAY DIFFRACTION99
2.0896-2.25090.14182220.12534902X-RAY DIFFRACTION99
2.2509-2.47740.17982510.13574722X-RAY DIFFRACTION96
2.4774-2.83580.16532460.15094915X-RAY DIFFRACTION99
2.8358-3.57230.15792730.13494914X-RAY DIFFRACTION99
3.5723-36.6440.13372440.13044949X-RAY DIFFRACTION98

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