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- PDB-1w7f: Crystal structure of the class A beta-lactamase BS3 inhibited wit... -

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Basic information

Entry
Database: PDB / ID: 1w7f
TitleCrystal structure of the class A beta-lactamase BS3 inhibited with isocitrate
ComponentsBETA-LACTAMASE
KeywordsHYDROLASE / BETA-LACTAMASE / ISOCITRATE / BACILLUS LICHENIFORMIS HYDROLASE
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / plasma membrane
Similarity search - Function
Beta-lactamase / Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. ...Beta-lactamase / Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOCITRIC ACID / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesBACILLUS LICHENIFORMIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPetrella, S. / Sauvage, E. / Herman, R. / Charlier, P.
Citation
Journal: To be Published
Title: Crystal Structure of the Class a Beta-Lactamase Bs3 Bs3 Inhibited with Isocitrate
Authors: Petrella, S. / Sauvage, E. / Herman, R. / Charlier, P.
#1: Journal: Biochemistry / Year: 2002
Title: Crystal Structure of the Bacillus Licheniformis Bs3 Class a Beta-Lactamase and of the Acyl-Enzyme Adduct Formed with Cefoxitin.
Authors: Fonze, E. / Vanhove, M. / Dives, G. / Sauvage, E. / Frere, J.M. / Charlier, P.
History
DepositionSep 1, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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)68,2153
Polymers68,0232
Non-polymers1921
Water3,819212
1
A: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2042
Polymers34,0121
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: BETA-LACTAMASE


Theoretical massNumber of molelcules
Total (without water)34,0121
Polymers34,0121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.896, 104.655, 63.766
Angle α, β, γ (deg.)90.00, 94.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein BETA-LACTAMASE


Mass: 34011.555 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BACILLUS LICHENIFORMIS (bacteria) / Strain: BS3
References: UniProt: P94458, UniProt: P00808*PLUS, beta-lactamase
#2: Chemical ChemComp-ICT / ISOCITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.64 Å3/Da / Density % sol: 53.1 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9796
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 10, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.8→63.2 Å / Num. obs: 52953 / % possible obs: 93.7 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.6 / % possible all: 85.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I2S

1i2s


Resolution: 1.8→19.88 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1262790.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.253 5367 10.1 %RANDOM
Rwork0.208 ---
obs0.208 52899 93.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.5144 Å2 / ksol: 0.416267 e/Å3
Displacement parametersBiso mean: 32 Å2
Baniso -1Baniso -2Baniso -3
1-1.78 Å20 Å2-1.82 Å2
2--2.52 Å20 Å2
3----4.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3990 0 13 212 4215
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it2.122
X-RAY DIFFRACTIONc_scbond_it2.112
X-RAY DIFFRACTIONc_scangle_it3.342.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.298 809 10.1 %
Rwork0.309 7174 -
obs--85 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5ICA_SP.PARAMICA_SP.TOP

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