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- PDB-1h5x: CRYSTAL STRUCTURE OF THE CLASS D BETA-LACTAMASE OXA-13 COMPLEXED ... -

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Basic information

Entry
Database: PDB / ID: 1h5x
TitleCRYSTAL STRUCTURE OF THE CLASS D BETA-LACTAMASE OXA-13 COMPLEXED WITH IMIPENEM
ComponentsBETA-LACTAMASE
KeywordsHYDROLASE / ACYL-ENZYME
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-IM2 / Beta-lactamase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMayer, C. / Pernot, L. / Sougakoff, W.
CitationJournal: To be Published
Title: Crystal Structure of the Acyl-Enzyme Intermediate Oxa-13:Imipenem
Authors: Pernot, L. / Mayer, C. / Sougakoff, W.
History
DepositionMay 29, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2002Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2011Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Dec 7, 2011Group: Non-polymer description
Revision 1.3Dec 13, 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-LACTAMASE
B: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9849
Polymers54,9012
Non-polymers1,0837
Water6,936385
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-78.4 kcal/mol
Surface area19580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.220, 82.060, 125.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9998, -0.0133, 0.0116), (-0.0121, 0.9957, 0.0921), (-0.0127, 0.092, -0.9957)
Vector: 45.4004, -5.1945, 119.5645)

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Components

#1: Protein BETA-LACTAMASE / / BETA-LACTAMASE OXA-13


Mass: 27450.260 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ACYL-ENZYME COMPLEX / Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Plasmid: PAZ304 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HB101 / References: UniProt: Q51400, beta-lactamase
#2: Chemical ChemComp-IM2 / (5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid / IMIPENEM, open form / N-FORMIMIDOYL-THIENAMYCINE, open form / Imipenem


Mass: 301.362 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N3O4S / Comment: antibiotic*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 385 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST NINETEEN RESIDUES ARE NOT PRESENT IN THE MATURE PROTEIN

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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: 2.3 Å3/Da / Density % sol: 47 %
Crystal growpH: 5.5
Details: 15-17% (W/V) PEG 4000, 0.1M SODIUM CACODYLATE PH 5.0-5.5, 0.2M LITHIUM SULFATE, PROTEIN 12-15 MG/ML

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 13, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 38825 / % possible obs: 93.8 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 36.6 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 15.9
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 1.3 / % possible all: 76.4

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMV. 6.0data reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H8Z

1h8z


Resolution: 1.9→40 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: IN CHAIN A THE RESIDUES FROM 92 - 100 AND IN CHAIN B THE RESIDUES FROM 93 - 104 WERE NOT INCLUDED IN THE REFINEMENT PROCESS THE RESIDUES SER A 20 AND SER B 20 WERE NOT SEEN IN THE ELECTRON DENSITY MAP.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1976 5 %RANDOM
Rwork0.212 ---
obs0.212 38788 93.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 39.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.38 Å20 Å20 Å2
2--5.69 Å20 Å2
3----2.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3679 0 65 385 4129
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.092
X-RAY DIFFRACTIONc_scbond_it1.982
X-RAY DIFFRACTIONc_scangle_it3.042.5
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.354 178 5.8 %
Rwork0.325 3036 -
obs--78.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4IMI2.PARAMIMI2.TOP

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