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- PDB-3blm: REFINED CRYSTAL STRUCTURE OF BETA-LACTAMASE FROM STAPHYLOCOCCUS A... -

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Basic information

Entry
Database: PDB / ID: 3blm
TitleREFINED CRYSTAL STRUCTURE OF BETA-LACTAMASE FROM STAPHYLOCOCCUS AUREUS PC1 AT 2.0
ComponentsBETA-LACTAMASE
KeywordsHYDROLASE
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Membrane lipoprotein, lipid attachment site / Prokaryotic membrane lipoprotein lipid attachment site / 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 ...Membrane lipoprotein, lipid attachment site / Prokaryotic membrane lipoprotein lipid attachment site / 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
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsHerzberg, O. / Moult, J.
Citation
Journal: J.Mol.Biol. / Year: 1991
Title: Refined crystal structure of beta-lactamase from Staphylococcus aureus PC1 at 2.0 A resolution.
Authors: Herzberg, O.
#1: Journal: Science / Year: 1987
Title: Bacterial Resistance to Beta-Lactam Antibiotics. Crystal Structure of Beta-Lactamase from Staphylococcus Aureus Pc1 at 2.5 Angstroms Resolution
Authors: Herzberg, O. / Moult, J.
#2: Journal: Biochem.J. / Year: 1985
Title: The Crystal Structure of Beta-Lactamase from Staphylococcus Aureus at 0.5Nm Resolution
Authors: Moult, J. / Sawyer, L. / Herzberg, O. / Jones, C.L. / Coulson, A.F.W. / Green, D.W. / Harding, M.M. / Ambler, R.P.
History
DepositionDec 3, 1990Processing site: BNL
SupersessionJan 15, 1991ID: 1BLM
Revision 1.0Jan 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-LACTAMASE


Theoretical massNumber of molelcules
Total (without water)28,8431
Polymers28,8431
Non-polymers00
Water3,729207
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.900, 94.000, 139.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-495-

HOH

21A-496-

HOH

31A-497-

HOH

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Components

#1: Protein BETA-LACTAMASE


Mass: 28843.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / References: UniProt: P00807, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 3.05 Å3/Da / Density % sol: 59.72 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
175-78 %satammonium sulfate1reservoir
20.3 M1reservoirKCl
30.1 M1reservoirNH4HCO3
40.3-0.6 %(w/v)PEG10001reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 3.63 Å / Num. all: 24339 / Num. measured all: 137958 / Rmerge(I) obs: 0.073 / Biso Wilson estimate: 23.2 Å2
Reflection shell
*PLUS
Mean I/σ(I) obs: 30.5

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.163 / Highest resolution: 2 Å
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2029 0 0 207 2236
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0230.023
X-RAY DIFFRACTIONp_angle_d0.0450.033
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0490.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0260.03
X-RAY DIFFRACTIONp_chiral_restr0.2130.2
X-RAY DIFFRACTIONp_singtor_nbd0.230.4
X-RAY DIFFRACTIONp_multtor_nbd0.1950.4
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2270.4
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.45
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Num. reflection obs: 17547 / σ(I): 2 / Highest resolution: 2 Å / Lowest resolution: 8 Å / Rfactor obs: 0.163
Solvent computation
*PLUS
Displacement parameters
*PLUS

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