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- PDB-1k56: OXA 10 class D beta-lactamase at pH 6.5 -

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Basic information

Entry
Database: PDB / ID: 1k56
TitleOXA 10 class D beta-lactamase at pH 6.5
Components(OXA10 beta-lactamase) x 2
KeywordsHYDROLASE / beta-lactamase / antibiotic resistance / carbamylation
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / 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
Beta-lactamase OXA-10
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsGolemi, D. / Maveyraud, L. / Vakulenko, S. / Samama, J.P. / Mobashery, S.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Critical involvement of a carbamylated lysine in catalytic function of class D beta-lactamases.
Authors: Golemi, D. / Maveyraud, L. / Vakulenko, S. / Samama, J.P. / Mobashery, S.
#1: Journal: Structure / Year: 2000
Title: Insights into class D beta-lactamases are revealed by the crystal structure of the OXA10 enzyme from Pseudomonas aeruginosa
Authors: Maveyraud, L. / Golemi, D. / Kotra, L.P. / Tranier, S. / Vakulenko, S. / Mobashery, S. / Samama, J.P.
#2: Journal: J.Am.Chem.Soc. / Year: 2000
Title: The first structural and mechanistic insights for class D beta-lactamases: evidence for a novel catalytic process for turnover of beta-lactam antibiotic
Authors: Golemi, D. / Maveyraud, L. / Vakulenko, S. / Tranier, S. / Ishiwata, A. / Kotra, L.P. / Samama, J.P. / Mobashery, S.
History
DepositionOct 10, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Database references
Revision 1.4Feb 5, 2014Group: Other
Revision 1.5Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OXA10 beta-lactamase
B: OXA10 beta-lactamase
C: OXA10 beta-lactamase
D: OXA10 beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,80310
Polymers110,2264
Non-polymers5766
Water12,322684
1
A: OXA10 beta-lactamase
C: OXA10 beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4235
Polymers55,1352
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-61 kcal/mol
Surface area19970 Å2
MethodPISA
2
B: OXA10 beta-lactamase
D: OXA10 beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3805
Polymers55,0922
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-57 kcal/mol
Surface area20240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.652, 82.430, 101.715
Angle α, β, γ (deg.)90.00, 95.49, 90.00
Int Tables number4
Space group name H-MP1211
Detailsthe biological assembly is a dimer. There are two dimers in the asymmetric unit : chains A and C form a dimer chains B and D form a dimer

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Components

#1: Protein OXA10 beta-lactamase / BETA-LACTAMASE PSE-2


Mass: 27567.293 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Residue 70 of chains A and B are KCX are carbamylated lysine. Residue 70 of chain C exists in two alternate conformations: KCX, carbamylated lysine, and lysine.
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P14489, beta-lactamase
#2: Protein OXA10 beta-lactamase / BETA-LACTAMASE PSE-2


Mass: 27524.291 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residue 70, LYS, is non-carbamylated. / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P14489, beta-lactamase
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 684 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE 70 OF CHAINS A AND B ARE KCX, CARBAMYLATED LYSINE. RESIDUE 70 OF CHAIN C EXISTS IN TWO ...RESIDUE 70 OF CHAINS A AND B ARE KCX, CARBAMYLATED LYSINE. RESIDUE 70 OF CHAIN C EXISTS IN TWO ALTERNATE CONFORMATIONS: KCX, CARBAMYLATED LYSINE AND LYSINE. RESIDUE 70 OF CHAIN D IS LYSINE.

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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: 2.52 Å3/Da / Density % sol: 51.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium sulphate, HEPES. Crystallization occured at pH 7.5. After obtaining the crystal, the pH was lowered to 6.5 for data collection., VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
220 mMsodium potassium phosphate1droppH7.8
32.0 Mammonium sulfate1reservoir
4100 mMTris-HCl1reservoirpH8.5, or 100mM Na/Hepes(pH7.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 4, 2001
RadiationMonochromator: Germanium Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.7→27.4 Å / Num. all: 118305 / Num. obs: 118305 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 20.383 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 12.2
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 4.1 / Num. unique all: 17487 / Rsym value: 0.341 / % possible all: 99.7
Reflection
*PLUS
Num. measured all: 307069
Reflection shell
*PLUS
% possible obs: 99.7 % / Num. unique obs: 17487 / Num. measured obs: 44375

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1E4D

1e4d


Resolution: 1.7→27 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: engh & huber
Details: In chains A and B, residue 70 is KCX, a carbamylated lysine (LYSINE NZ-CARBOXYLIC ACID). In chain C, residue 70 exists in two conformations: conformation A, as KCX, and conformation B, as ...Details: In chains A and B, residue 70 is KCX, a carbamylated lysine (LYSINE NZ-CARBOXYLIC ACID). In chain C, residue 70 exists in two conformations: conformation A, as KCX, and conformation B, as LYS. In chain D, residue 70 is a lysine. Water molecule 240 is associated with conformation B of Lys70C.
RfactorNum. reflection% reflectionSelection details
Rfree0.22068 2364 2 %RANDOM
Rwork0.18334 ---
all0.18408 117716 --
obs0.18408 117716 97.8 %-
Displacement parametersBiso mean: 16.621 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20.09 Å2
2---0.01 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.7→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7597 0 30 684 8311
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.021
X-RAY DIFFRACTIONp_mcbond_it1.2671.5
X-RAY DIFFRACTIONp_mcangle_it1.9442
X-RAY DIFFRACTIONp_scbond_it2.7653
X-RAY DIFFRACTIONp_scangle_it4.1044.5
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 27 Å / σ(F): 0 / % reflection Rfree: 2 % / Rfactor obs: 0.18344
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.686
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg16.034

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