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- PDB-5mmy: Crystal structure of OXA10 with HEPES -

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Basic information

Entry
Database: PDB / ID: 5mmy
TitleCrystal structure of OXA10 with HEPES
ComponentsBeta-lactamase OXA-10
KeywordsHYDROLASE / antibiotic resistance oxacillinase carbapenems
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic
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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CARBONATE ION / Beta-lactamase OXA-10
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.88 Å
AuthorsBrem, J.
CitationJournal: Org. Biomol. Chem. / Year: 2017
Title: (13)C-Carbamylation as a mechanistic probe for the inhibition of class D beta-lactamases by avibactam and halide ions.
Authors: Lohans, C.T. / Wang, D.Y. / Jorgensen, C. / Cahill, S.T. / Clifton, I.J. / McDonough, M.A. / Oswin, H.P. / Spencer, J. / Domene, C. / Claridge, T.D.W. / Brem, J. / Schofield, C.J.
History
DepositionDec 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase OXA-10
B: Beta-lactamase OXA-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,12511
Polymers55,2832
Non-polymers8429
Water5,441302
1
A: Beta-lactamase OXA-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4249
Polymers27,6411
Non-polymers7828
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase OXA-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7012
Polymers27,6411
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.772, 102.189, 127.409
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Beta-lactamase OXA-10 / Beta-lactamase PSE-2


Mass: 27641.438 Da / Num. of mol.: 2 / Mutation: Lys70KCX
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: bla, oxa10, pse2 / Plasmid: pet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14489, beta-lactamase

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Non-polymers , 7 types, 311 molecules

#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 3.2 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M HEPES pH 7.0, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 28, 2015 / Details: mirror
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.88→79.72 Å / Num. obs: 52703 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 18.083 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.051 / Rrim(I) all: 0.183 / Net I/σ(I): 11.8 / Num. measured all: 679292 / Scaling rejects: 548
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.88-1.9312.92.0923.20.862199.8
8.41-79.7211.50.06423.70.9981100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.82 Å79.72 Å
Translation5.82 Å79.72 Å

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Processing

Software
NameVersionClassification
Aimless0.5.17data scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FQ9

5fq9


Resolution: 1.88→8.41 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1979 --
Rwork0.1778 --
obs-52703 100 %
Displacement parametersBiso max: 104.28 Å2 / Biso mean: 32.085 Å2 / Biso min: 6.74 Å2
Refinement stepCycle: LAST / Resolution: 1.88→8.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3774 0 52 302 4128

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