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- PDB-1k6r: STRUCTURE OF THE CLASS D BETA-LACTAMASE OXA-10 IN COMPLEX WITH MO... -

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Basic information

Entry
Database: PDB / ID: 1k6r
TitleSTRUCTURE OF THE CLASS D BETA-LACTAMASE OXA-10 IN COMPLEX WITH MOXALACTAM
ComponentsBeta-lactamase PSE-2
KeywordsHYDROLASE / beta-lactamase / moxalactam / class D
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
Chem-MX1 / Beta-lactamase OXA-10
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKerff, F. / Fonze, E. / Sauvage, E. / Frere, J.M. / Charlier, P.
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF CLASS D BETA-LACTAMASE OXA-10 IN COMPLEX WITH DIFFERENT SUBSTRATES AND ONE INHIBITOR.
Authors: Kerff, F. / Fonze, E. / Sauvage, E. / Frere, J.M. / Charlier, P.
History
DepositionOct 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 31, 2011Group: Non-polymer description
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase PSE-2
B: Beta-lactamase PSE-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2704
Polymers55,4252
Non-polymers8452
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint6 kcal/mol
Surface area18990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.706, 96.003, 125.195
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer in the asymmetric unit formed by chains A and B

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Components

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


Mass: 27712.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: plasmid pMON234 / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P14489, beta-lactamase
#2: Chemical ChemComp-MX1 / (2R)-2-((R)-CARBOXY{[CARBOXY(4-HYDROXYPHENYL)ACETYL]AMINO}METHOXYMETHYL)-5-METHYLENE-5,6-DIHYDRO-2H-1,3-OXAZINE-4-CARBO XYLIC ACID / MOXALACTAM (HYDROLYZED)


Mass: 422.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H18N2O10
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
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: 2.64 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: AMMONIUM SULFATE, BICINE PH 9, SOAKING AT PH 7 WITH HEPES, PEG400, MOXALACTAM, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 12, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→32.9 Å / Num. all: 34358 / Num. obs: 34358 / % possible obs: 97.9 % / Redundancy: 5 % / Biso Wilson estimate: 28.3 Å2 / Rsym value: 0.077 / Net I/σ(I): 6.4
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 4765 / Rsym value: 0.49 / % possible all: 94.5

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K4F

1k4f


Resolution: 2.3→29.76 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1883343.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.237 2587 9.9 %RANDOM
Rwork0.198 ---
obs0.198 26040 96.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.1292 Å2 / ksol: 0.384554 e/Å3
Displacement parametersBiso mean: 41.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.63 Å20 Å20 Å2
2--8.78 Å20 Å2
3----11.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3725 0 58 186 3969
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.432
X-RAY DIFFRACTIONc_scbond_it2.132
X-RAY DIFFRACTIONc_scangle_it3.162.5
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.271 239 9.8 %
Rwork0.235 2189 -
obs-2189 92.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_PSE.PARAMPROTEIN-PSE.TOP
X-RAY DIFFRACTION2MOXA-LD.PARAMMOXA-LD.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

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