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- PDB-1k54: OXA-10 class D beta-lactamase partially acylated with reacted 6be... -

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Basic information

Entry
Database: PDB / ID: 1k54
TitleOXA-10 class D beta-lactamase partially acylated with reacted 6beta-(1-hydroxy-1-methylethyl) penicillanic acid
Components(Beta lactamase OXA- ...) 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 / periplasmic space / response to antibiotic / plasma membrane
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
Chem-HOQ / 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: Derived calculations / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
Revision 1.5Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_distant_solvent_atoms / pdbx_entry_details ...pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn

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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)112,74329
Polymers110,1834
Non-polymers2,56025
Water14,790821
1
A: Beta lactamase OXA-10
C: Beta lactamase OXA-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,26213
Polymers55,0922
Non-polymers1,17011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Beta lactamase OXA-10
D: Beta lactamase OXA-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,48216
Polymers55,0922
Non-polymers1,39014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)66.649, 82.480, 101.957
Angle α, β, γ (deg.)90.00, 95.38, 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

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Beta lactamase OXA- ... , 2 types, 4 molecules ABCD

#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 is KCX, carbamylated lysine. Acylated at SER 67.
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
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

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Non-polymers , 4 types, 846 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-HOQ / (1R)-2-(1-CARBOXY-2-HYDROXY-2-METHYL-PROPYL)-5,5-DIMETHYL-THIAZOLIDINE-4-CARBOXYLIC ACID


Mass: 277.337 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H19NO5S
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 821 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 51.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium sulafate, 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: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 27, 2000
RadiationMonochromator: diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.7→44.77 Å / Num. all: 119631 / Num. obs: 119631 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 20.115 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 12.9
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 3.2 / Num. unique all: 16474 / Rsym value: 0.289 / % possible all: 93.8
Reflection
*PLUS
Num. measured all: 432971
Reflection shell
*PLUS
% possible obs: 93.8 % / Num. unique obs: 16474 / Num. measured obs: 45364

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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→44.77 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: engh & huber
RfactorNum. reflection% reflectionSelection details
Rfree0.21043 1794 1.5 %RANDOM
Rwork0.17688 ---
all0.17738 119608 --
obs0.17738 119608 99.05 %-
Displacement parametersBiso mean: 16.799 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å20.03 Å2
2---0.2 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.7→44.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7614 0 143 821 8578
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.191
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.558
X-RAY DIFFRACTIONp_mcangle_it1.015
X-RAY DIFFRACTIONp_scbond_it1.376
X-RAY DIFFRACTIONp_scangle_it2.273
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
LS refinement shellHighest resolution: 1.7 Å / Rfactor Rfree: 0.277 / Rfactor Rwork: 0.225 / Total num. of bins used: 20
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 1.5 % / Rfactor obs: 0.17688
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.006
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg14.341

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