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- PDB-1bsg: BETA-LACTAMASE FROM STREPTOMYCES ALBUS G -

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Basic information

Entry
Database: PDB / ID: 1bsg
TitleBETA-LACTAMASE FROM STREPTOMYCES ALBUS G
ComponentsBETA LACTAMASEBeta-lactamase
KeywordsHYDROLASE / ANTIBIOTIC RESISTANCE / PENICILLIN
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase, class-A / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Beta-lactamase
Similarity search - Component
Biological speciesStreptomyces albus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.85 Å
AuthorsFonze, E. / Charlier, P. / Dideberg, O.
History
DepositionJul 20, 1998-
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8112
Polymers28,7521
Non-polymers591
Water4,342241
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)40.630, 43.570, 138.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein BETA LACTAMASE / Beta-lactamase / PENICILLINASE


Mass: 28752.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces albus (bacteria) / Strain: G / References: UniProt: P14559, beta-lactamase
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionBiso Wilson estimate: 8.6 Å2

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
RefinementResolution: 1.85→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.152 --
obs0.152 16921 78.82 %
Displacement parametersBiso mean: 14.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.14 Å
Refinement stepCycle: LAST / Resolution: 1.85→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2018 0 4 241 2263
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.412
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.25
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.381.5
X-RAY DIFFRACTIONx_mcangle_it2.012
X-RAY DIFFRACTIONx_scbond_it2.872
X-RAY DIFFRACTIONx_scangle_it4.532.5
LS refinement shellResolution: 1.85→1.93 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.1767 1541 -
obs--58.66 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2TIP3P.PARAMETERTIP3P.TOPOLOGY

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