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- PDB-1bue: NMC-A CARBAPENEMASE FROM ENTEROBACTER CLOACAE -

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Basic information

Entry
Database: PDB / ID: 1bue
TitleNMC-A CARBAPENEMASE FROM ENTEROBACTER CLOACAE
ComponentsPROTEIN (IMIPENEM-HYDROLYSING BETA-LACTAMASE)
KeywordsHYDROLASE / ANTIBIOTIC RESISTANCE / CLASS A CARBAPENEMASE
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / response to antibiotic
Similarity search - Function
Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Imipenem-hydrolyzing beta-lactamase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.64 Å
AuthorsSwaren, P. / Maveyraud, L. / Cabantous, S. / Pedelacq, J.D. / Mourey, L. / Frere, J.M. / Samama, J.P.
Citation
Journal: J.Biol.Chem. / Year: 1998
Title: X-ray analysis of the NMC-A beta-lactamase at 1.64-A resolution, a class A carbapenemase with broad substrate specificity.
Authors: Swaren, P. / Maveyraud, L. / Raquet, X. / Cabantous, S. / Duez, C. / Pedelacq, J.D. / Mariotte-Boyer, S. / Mourey, L. / Labia, R. / Nicolas-Chanoine, M.H. / Nordmann, P. / Frere, J.M. / Samama, J.P.
#1: Journal: FEMS Microbiol.Lett. / Year: 1996
Title: A Kinetic Study of NMC-A Beta-Lactamase, an Ambler Class A Carbapenemase Also Hydrolyzing Cephamycins
Authors: Mariotte-Boyer, S. / Nicolas-Chanoine, M.H. / Labia, R.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Analysis of a Carbapenem-Hydrolyzing Class A Beta-Lactamase from Enterobacter Cloacae and of its Lysr-Type Regulatory Protein
Authors: Naas, T. / Nordmann, P.
History
DepositionSep 3, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 2, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (IMIPENEM-HYDROLYSING BETA-LACTAMASE)


Theoretical massNumber of molelcules
Total (without water)29,1381
Polymers29,1381
Non-polymers00
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.690, 52.900, 67.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PROTEIN (IMIPENEM-HYDROLYSING BETA-LACTAMASE) / CARBAPENEMASE / NMC-A


Mass: 29137.596 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Strain: NOR-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52663, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 45.6 %
Description: ONE CRYSTAL WAS USED FOR NATIVE LOW RESOLUTION DATA TO 2.9 ANGSTROMS RESOLUTION, AND A SECOND CRYSTAL WAS USED FOR DATA TO 1.64 ANGSTROMS RESOLUTION.
Crystal growpH: 5.25
Details: INITIAL PROTEIN CONCENTRATION WAS 2.0 G/L EQUILIBRATED AGAINST 0.200 M MES PH 5.25, 20% (W/V)PEG 1500, 6% (V/V) N-PROPANOL AT 295K.
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.0 mg/mlprotein1drop
245 mMMES1drop
35 %(w/v)PEG15001drop
4200 mMMES1reservoir
520 %(w/v)PEG15001reservoir
66 %(v/v)n-propyl alcohol1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.975
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 7, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.64→31 Å / Num. obs: 32762 / % possible obs: 93.3 % / Redundancy: 4.1 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 33.3
Reflection shellResolution: 1.64→1.68 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 7.1 / Rsym value: 0.192 / % possible all: 68
Reflection
*PLUS
Num. measured all: 111487

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
CCP4data reduction
CCP4model building
X-PLORmodel building
X-PLOR3.1refinement
CCP4data scaling
CCP4phasing
X-PLORphasing
RefinementMethod to determine structure: SIRAS
Starting model: NOT APPLICABLE

Resolution: 1.64→31 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT CORRECTION USED WITH A DENSITY OF 0.34 E-/A**3, SOLVENT RADIUS OF 0.25 ANGSTROMS AND B FACTORS OF 50 A**2 RESIDUES 30 AND 63 HAVE ALTERNATE CONFORMATIONS. RESIDUE 140A WAS INSERTED.
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1623 5 %RANDOM
Rwork0.192 ---
obs0.192 32739 93.3 %-
Displacement parametersBiso mean: 13.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å / Luzzati d res low obs: 31 Å / Luzzati sigma a obs: 0.16 Å
Refinement stepCycle: LAST / Resolution: 1.64→31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2028 0 0 115 2143
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.297
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.37
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.126
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: NOT APPLICABLE
LS refinement shellResolution: 1.64→1.71 Å / Total num. of bins used: 8 / % reflection obs: 74.3 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 13.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.37
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.126

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