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- PDB-1k57: OXA 10 class D beta-lactamase at pH 6.0 -

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Basic information

Entry
Database: PDB / ID: 1k57
TitleOXA 10 class D beta-lactamase at pH 6.0
Components(BETA LACTAMASE OXA-10) 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: 1.9 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 1.3Aug 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 1.4Nov 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: BETA LACTAMASE OXA-10
B: BETA LACTAMASE OXA-10
C: BETA LACTAMASE OXA-10
D: BETA LACTAMASE OXA-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,24015
Polymers110,1834
Non-polymers1,05711
Water10,557586
1
A: BETA LACTAMASE OXA-10
C: BETA LACTAMASE OXA-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5727
Polymers55,0922
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-82 kcal/mol
Surface area20530 Å2
MethodPISA
2
B: BETA LACTAMASE OXA-10
D: BETA LACTAMASE OXA-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6688
Polymers55,0922
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-88 kcal/mol
Surface area20510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.755, 82.520, 101.791
Angle α, β, γ (deg.)90.00, 95.50, 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 BETA LACTAMASE OXA-10 / BETA-LACTAMASE PSE-2


Mass: 27567.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Residue 70, KCX, is CARBAMYLATED 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 BETA LACTAMASE OXA-10 / BETA-LACTAMASE PSE-2


Mass: 27524.291 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Residue 70, LYS, is not 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.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 586 / 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: 2.53 Å3/Da / Density % sol: 51.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: ammonium sulfate, HEPES. Crystallization occured at pH 7.5. After obtaining the crystal, the pH was lowered to 6.0 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, 2000
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: 1.9→33.77 Å / Num. all: 84615 / Num. obs: 84615 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 9.7
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 3 / Num. unique all: 11824 / Rsym value: 0.404 / % possible all: 94
Reflection
*PLUS
Num. measured all: 215405
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 2 Å / % possible obs: 94 % / Num. unique obs: 11824 / Num. measured obs: 26849

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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: 1.9→33.77 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. In chains C and D, residue 70 is a lysine and is not carbamylated.
RfactorNum. reflection% reflectionSelection details
Rfree0.22234 1693 2 %RANDOM
Rwork0.17941 ---
all0.18026 84560 --
obs0.18026 84560 97.6 %-
Displacement parametersBiso mean: 19.764 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å2-0.21 Å2
2---0.13 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.9→33.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7663 0 55 586 8304
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0230.022
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.1811.5
X-RAY DIFFRACTIONp_mcangle_it2.0752
X-RAY DIFFRACTIONp_scbond_it3.2783
X-RAY DIFFRACTIONp_scangle_it5.2084.5
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / σ(F): 0 / % reflection Rfree: 2 % / Rfactor obs: 0.17941
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.931
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg16.642

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