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- PDB-1blp: STRUCTURAL BASIS FOR THE INACTIVATION OF THE P54 MUTANT OF BETA-L... -

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Basic information

Entry
Database: PDB / ID: 1blp
TitleSTRUCTURAL BASIS FOR THE INACTIVATION OF THE P54 MUTANT OF BETA-LACTAMASE FROM STAPHYLOCOCCUS AUREUS PC1
ComponentsBETA-LACTAMASE
KeywordsHYDROLASE(ACTING ON CYCLIC AMIDES)
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: 2.3 Å
AuthorsHerzberg, O.
Citation
Journal: Biochemistry / Year: 1991
Title: Structural basis for the inactivation of the P54 mutant of beta-lactamase from Staphylococcus aureus PC1.
Authors: Herzberg, O. / Kapadia, G. / Blanco, B. / Smith, T.S. / Coulson, A.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Refined Crystal Structure of Beta-Lactamase from Staphylococcus Aureus Pc1 at 2.0
Authors: Herzberg, O.
#2: 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.
#3: 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
DepositionSep 23, 1993Processing site: BNL
Revision 1.0Apr 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 23, 2011Group: Structure summary
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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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)28,8421
Polymers28,8421
Non-polymers00
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.900, 96.000, 137.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein BETA-LACTAMASE


Mass: 28842.227 Da / Num. of mol.: 1 / Mutation: D170N
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.: 126 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE ACTIVE SITE SERINE IS SER 70. THERE IS AN OXYANION HOLE FORMED BY THE MAIN CHAIN NITROGEN ATOMS ...THE ACTIVE SITE SERINE IS SER 70. THERE IS AN OXYANION HOLE FORMED BY THE MAIN CHAIN NITROGEN ATOMS OF SER 70 AND GLN 237, IN A SIMILAR MANNER TO THE SERINE PROTEASE STRUCTURES.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 60.91 %
Crystal grow
*PLUS
pH: 8 / Method: unknown / Details: Herzberg, O., (1987) Science, 236, 694.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
178 %satammonium sulfate11
20.3 M11KCl
3100 mM11NH4HCO3

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 4.18 Å / Num. all: 16519 / Num. measured all: 52480 / Rmerge(I) obs: 0.084
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.44 Å / Num. possible: 2694 / Num. measured obs: 6138 / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 18.4

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.3→6 Å / σ(F): 2 /
RfactorNum. reflection
obs0.181 122189
Refinement stepCycle: LAST / Resolution: 2.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1982 0 0 126 2108
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0230.025
X-RAY DIFFRACTIONp_angle_d0.0420.036
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.040.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.0980.112
X-RAY DIFFRACTIONp_mcangle_it0.1310.138
X-RAY DIFFRACTIONp_scbond_it0.1260.138
X-RAY DIFFRACTIONp_scangle_it0.1590.159
X-RAY DIFFRACTIONp_plane_restr0.0240.03
X-RAY DIFFRACTIONp_chiral_restr0.2260.2
X-RAY DIFFRACTIONp_singtor_nbd0.2380.4
X-RAY DIFFRACTIONp_multtor_nbd0.2120.4
X-RAY DIFFRACTIONp_xhyhbond_nbd0.260.4
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.95
X-RAY DIFFRACTIONp_staggered_tor24.4120
X-RAY DIFFRACTIONp_orthonormal_tor21.9120
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.5 Å / Total num. of bins used: 7 / Rfactor obs: 0.249

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