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- PDB-1k55: OXA 10 class D beta-lactamase at pH 7.5 -

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Basic information

Entry
Database: PDB / ID: 1k55
TitleOXA 10 class D beta-lactamase at pH 7.5
Components(Beta lactamase OXA-10) x 2
KeywordsHYDROLASE / beta-lactamase / antibiotic resistance / carbamylation
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
Beta-lactamase OXA-10
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.39 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)112,47131
Polymers110,1834
Non-polymers2,28827
Water16,970942
1
A: Beta lactamase OXA-10
C: Beta lactamase OXA-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,04613
Polymers55,0922
Non-polymers95511
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-96 kcal/mol
Surface area20300 Å2
MethodPISA
2
B: Beta lactamase OXA-10
D: Beta lactamase OXA-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,42518
Polymers55,0922
Non-polymers1,33316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-108 kcal/mol
Surface area20880 Å2
MethodPISA
3
C: Beta lactamase OXA-10
hetero molecules

B: Beta lactamase OXA-10
hetero molecules

A: Beta lactamase OXA-10
D: Beta lactamase OXA-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,47131
Polymers110,1834
Non-polymers2,28827
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation2_546-x,y-1/2,-z+11
crystal symmetry operation2_545-x,y-1/2,-z1
identity operation1_555x,y,z1
Buried area8700 Å2
ΔGint-231 kcal/mol
Surface area42390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.514, 82.285, 101.713
Angle α, β, γ (deg.)90.00, 95.44, 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 OF CHAINS A AND B, KCX ARE CARBAMYLATED LYSINE.
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Plasmid: pET24a / 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


Mass: 27524.291 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: RESIDUE 70 OF CHAINS C AND D EXISTS IN TWO ALTERNATE CONFORMATIONS: KCX, CARBAMYLATED LYSINE, AND LYSINE.
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Plasmid: pET24a / 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


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 942 / 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: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium sulphate, HEPES, pH 7.5, 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: Jun 6, 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: 1.39→53.16 Å / Num. all: 216019 / Num. obs: 216019 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 11.8
Reflection shellResolution: 1.39→1.47 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 3.3 / Num. unique all: 29650 / Rsym value: 0.373 / % possible all: 99
Reflection
*PLUS
Num. measured all: 841487
Reflection shell
*PLUS
% possible obs: 93.3 % / Num. unique obs: 29650 / Num. measured obs: 95038

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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: 1.39→53.16 Å / Isotropic thermal model: overall anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: engh & huber
Details: SUL 1024, which is assigned alternate position B, corresponds to alternate conformation B of chain D residue 115. Chain C: the following residues display alternate conformations for side ...Details: SUL 1024, which is assigned alternate position B, corresponds to alternate conformation B of chain D residue 115. Chain C: the following residues display alternate conformations for side chain atoms only : Thr23C S60C, Glu195C, Glu231C and Ser245C. Chain D: the following residues display alternate conformations for side chain atoms only : Ser33C Ser60D, Glu86D, Arg125D, Ser147D, Ser179D, Glu183D. Gly265D and Gly266D display alternate conformations of the dipeptide. chains C and D: Other residues in alternate conformation correspond to two distinct conformations of the enzyme: conformations A and B : Met99C, Lys100C, Gln101C, Trp102C, Glu103C, Val114C, Ser115C, Ala116C, Val117C and Pro118C. RESIDUE 70 EXISTS IN TWO CONFORMATIONS: CONFORMATION A, AS a classical non modified LYS residue, AND CONFORMATION B, AS KCX, a carbamylated lysine,in chains C and D. There is no density accounting for conformation B of residues Arg97 C and D, Ala98 C and D and Met99D, but these residues are necessarly in an alternate conformation for sterical reasons.
RfactorNum. reflection% reflectionSelection details
Rfree0.1809 2165 1 %random
Rwork0.15311 ---
all0.15339 215989 --
obs0.15339 215989 98.92 %-
Displacement parametersBiso mean: 14.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20.07 Å2
2---0.17 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.39→53.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7958 0 131 942 9031
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_deg1.581
LS refinement shellResolution: 1.39→1.427 Å
RfactorNum. reflection% reflection
Rfree0.267 126 1 %
Rwork0.241 --
obs-13790 -
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 1 % / Rfactor obs: 0.15311 / Rfactor Rfree: 0.1809
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg15.744

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