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- PDB-1blh: STRUCTURE OF A PHOSPHONATE-INHIBITED BETA-LACTAMASE. AN ANALOG OF... -

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Basic information

Entry
Database: PDB / ID: 1blh
TitleSTRUCTURE OF A PHOSPHONATE-INHIBITED BETA-LACTAMASE. AN ANALOG OF THE TETRAHEDRAL TRANSITION STATE(SLASH)INTERMEDIATE OF BETA-LACTAM HYDROLYSIS
ComponentsBETA-LACTAMASE
KeywordsHYDROLASE(BETA-LACTAMASE)
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / 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
[[N-(BENZYLOXYCARBONYL)AMINO]METHYL]PHOSPHATE / Beta-lactamase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsChen, C.C.H. / Herzberg, O.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: Structure of a phosphonate-inhibited beta-lactamase. An analog of the tetrahedral transition state/intermediate of beta-lactam hydrolysis.
Authors: Chen, C.C. / Rahil, J. / Pratt, R.F. / Herzberg, O.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: Inhibition of Beta-Lactamase by Clavulanate. Trapped Intermediates in Cryocrystallographic Studies
Authors: Chen, C.C.H. / Herzberg, O.
#2: Journal: J.Mol.Biol. / Year: 1991
Title: Refined Crystal Structure of Beta-Lactamase from Staphylococcus Aureus Pc1 at 2.0 Angstroms Resolution
Authors: Herzberg, O.
#3: 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.
#4: Journal: Curr.Opin.Struct.Biol. / Year: 1991
Title: Penicillin-Binding and Degrading Enzymes
Authors: Herzberg, O. / Moult, J.
#5: 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.
#6: 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 30, 1993Processing site: BNL
Revision 1.0Aug 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
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_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)29,0882
Polymers28,8431
Non-polymers2451
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.960, 94.200, 138.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Atom site foot note1: GLU 166 - ILE 167 OMEGA = 1.57 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
Components on special symmetry positions
IDModelComponents
11A-494-

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: Chemical ChemComp-FOS / [[N-(BENZYLOXYCARBONYL)AMINO]METHYL]PHOSPHATE


Mass: 245.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12NO5P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 59.8 %
Crystal grow
*PLUS
pH: 8 / Method: unknown
Details: referred to 'Herzberg, O.', (1987) Science, 236, 694-701
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 / Num. all: 16164 / Num. obs: 14163 / Num. measured all: 46421 / Biso Wilson estimate: 26.4 Å2

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.3→8 Å / Rfactor obs: 0.166 / σ(F): 2
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1999 0 15 195 2209
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.025
X-RAY DIFFRACTIONp_angle_d0.040.036
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0370.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.0890.112
X-RAY DIFFRACTIONp_mcangle_it0.1190.138
X-RAY DIFFRACTIONp_scbond_it0.1180.138
X-RAY DIFFRACTIONp_scangle_it0.150.159
X-RAY DIFFRACTIONp_plane_restr0.0220.03
X-RAY DIFFRACTIONp_chiral_restr0.1870.2
X-RAY DIFFRACTIONp_singtor_nbd0.2880.4
X-RAY DIFFRACTIONp_multtor_nbd0.2030.4
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2260.4
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.95
X-RAY DIFFRACTIONp_staggered_tor21.9120
X-RAY DIFFRACTIONp_orthonormal_tor24.5120
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 11735 / Rfactor obs: 0.166
Solvent computation
*PLUS
Displacement parameters
*PLUS

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