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- PDB-1blc: INHIBITION OF BETA-LACTAMASE BY CLAVULANATE: TRAPPED INTERMEDIATE... -

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Basic information

Entry
Database: PDB / ID: 1blc
TitleINHIBITION OF BETA-LACTAMASE BY CLAVULANATE: TRAPPED INTERMEDIATES IN CRYOCRYSTALLOGRAPHIC STUDIES
ComponentsBETA-LACTAMASE
KeywordsHYDROLASE(ACTING IN CYCLIC AMIDES)
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
Chem-CEM / Chem-TEM / Beta-lactamase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsChen, C.C.H. / Herzberg, O.
Citation
Journal: J.Mol.Biol. / Year: 1992
Title: Inhibition of beta-lactamase by clavulanate. Trapped intermediates in cryocrystallographic studies.
Authors: Chen, C.C. / Herzberg, O.
#1: Journal: To be Published
Title: Structure of a Phosphonate-Inhibited Beta-Lactamase: An Analog of the Tetrahedral Transition State(Slash)Intermediate of Beta-Lactam Hydrolysis
Authors: Chen, C.C.H. / Rahil, J. / Pratt, R.F. / 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: J.Biochem.(Tokyo) / 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 27, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 10, 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 16, 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)29,2984
Polymers28,8431
Non-polymers4543
Water5,837324
1
A: BETA-LACTAMASE
hetero molecules

A: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5958
Polymers57,6862
Non-polymers9096
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)54.100, 88.000, 141.300
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 CIS PEPTIDE BOND.
2: SIDE CHAINS AND DERIVATIVES HAVE BEEN MODELLED IN TWO ALTERNATE CONFORMATIONS AND ASSIGNED ALTERNATE LOCATION INDICATORS *A* AND *B*.
Components on special symmetry positions
IDModelComponents
11A-436-

HOH

21A-606-

HOH

31A-619-

HOH

41A-623-

HOH

51A-624-

HOH

61A-625-

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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CEM / N-(1-CARBOXY-2-HYDROXY-4-OXO-BUTYL)-N-(3-OXO-CISPROPENYL)AMINE


Mass: 201.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11NO5
#4: Chemical ChemComp-TEM / N-(2-HYDROXY-4-OXO-BUTYL)-N-(3-OXO-TRANSPROPENYL)AMINE


Mass: 157.167 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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
Nonpolymer detailsTHERE ARE TWO CLAVULANATE DEGRADATION PRODUCTS, COVALENTLY BOUND TO SER 70, AND ALTERNATELY ...THERE ARE TWO CLAVULANATE DEGRADATION PRODUCTS, COVALENTLY BOUND TO SER 70, AND ALTERNATELY OCCUPYING THE ACTIVE SITE. THESE HAVE BEEN INTERPRETED AS CIS AND TRANS ENAMINES. THE TRANS ENAMINE LACKS A CARBOXYLATE GROUP. THE CIS ENAMINE IS LABELLED CEM AND THE TRANS ENAMINE IS LABELLED TEM (*INC* AND *INT*, RESPECTIVELY, IN THE PAPER CITED ON *JRNL* RECORDS ABOVE). THE OG ATOM OF SER 70 ADOPTS ALTERNATE LOCATIONS, WHICH ARE REPRESENTED BY THE ALTERNATE LOCATION INDICATORS *A* AND *B*. *A* CORRESPONDS TO THE BINDING TO CEM, AND *B* TO THE BINDING TO TEM. THE INHIBITOR, SULFATE ION, AND WATER MOLECULES ARE GIVEN IN THE HETATM LIST. THE WATER MOLECULES ARE LISTED IN DECREASING ORDER OF OCCUPANCY**2/B, AND ARE NUMBERED STARTING FROM 301 INSTEAD OF FROM 1, AS IN THE PUBLICATION CITED IN THE *JRNL* RECORDS ABOVE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.8 %
Crystal grow
*PLUS
pH: 8 / Method: unknown
Details: referred to 'Moult, J.', (1985) Biochem.J., 225, 167.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
160-75 %satammonium sulfate11
210-20 mg/mlprotein11

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Data collection

DiffractionMean temperature: 120 K
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.05 Å / Lowest resolution: 3.72 Å / Num. all: 21726 / % possible obs: 97 % / Observed criterion σ(I): 2 / Num. measured all: 46421 / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
Highest resolution: 2.05 Å / Lowest resolution: 2.17 Å / % possible obs: 96 % / Num. possible: 3557 / Num. measured obs: 1635 / Rmerge(I) obs: 0.072 / Mean I/σ(I) obs: 31.5

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.2→6 Å / σ(F): 2 /
RfactorNum. reflection
obs0.179 14015
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2030 0 30 324 2384
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0220.025
X-RAY DIFFRACTIONp_angle_d0.0410.036
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0360.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.090.112
X-RAY DIFFRACTIONp_mcangle_it0.1170.138
X-RAY DIFFRACTIONp_scbond_it0.1190.138
X-RAY DIFFRACTIONp_scangle_it0.1480.159
X-RAY DIFFRACTIONp_plane_restr0.0240.03
X-RAY DIFFRACTIONp_chiral_restr0.2430.2
X-RAY DIFFRACTIONp_singtor_nbd0.2440.4
X-RAY DIFFRACTIONp_multtor_nbd0.2550.4
X-RAY DIFFRACTIONp_xhyhbond_nbd0.280.4
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.15
X-RAY DIFFRACTIONp_staggered_tor24.9120
X-RAY DIFFRACTIONp_orthonormal_tor28.6120
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 6 Å / Num. reflection obs: 14015 / σ(F): 2 / Rfactor all: 0.199 / Rfactor obs: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.5 Å / Rfactor all: 0.21 / Rfactor obs: 0.178

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