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- PDB-1mbl: A catalytically-impaired class A beta-lactamase: 2 Angstroms crys... -

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Basic information

Entry
Database: PDB / ID: 1mbl
TitleA catalytically-impaired class A beta-lactamase: 2 Angstroms crystal structure and kinetics of the Bacillus licheniformis E166A mutant
ComponentsBETA-LACTAMASE
KeywordsHYDROLASE
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / plasma membrane
Similarity search - Function
Beta-lactamase / 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. ...Beta-lactamase / 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 speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsKnox, J.R. / Moews, P.C.
Citation
Journal: Protein Eng. / Year: 1993
Title: A catalytically-impaired class A beta-lactamase: 2 A crystal structure and kinetics of the Bacillus licheniformis E166A mutant.
Authors: Knox, J.R. / Moews, P.C. / Escobar, W.A. / Fink, A.L.
#1: Journal: RECENT ADVANCES IN THE CHEMISTRY OF ANTI-INFECTIVE AGENTS (SPEC.PUBL.R.SOC.CHEM.,NO. 119)
Year: 1993
Title: Crystallography of Penicillin-Binding Enzymes
Authors: Knox, J.R.
#2: Journal: J.Mol.Biol. / Year: 1991
Title: Beta-Lactamase of Bacillus Licheniformis 749C: Refinement at 2 Angstroms Resolution and Analysis of Hydration
Authors: Knox, J.R. / Moews, P.C.
History
DepositionAug 17, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 30, 2011Group: Structure summary
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-LACTAMASE
B: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0584
Polymers56,8662
Non-polymers1922
Water10,431579
1
A: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5292
Polymers28,4331
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5292
Polymers28,4331
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.200, 94.100, 43.800
Angle α, β, γ (deg.)90.00, 104.50, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO A 167 / 2: CIS PROLINE - PRO B 167
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.876177, -0.033827, -0.480802), (0.034703, -0.999373, 0.007071), (-0.480739, -0.010489, 0.876801)
Vector: 62.9458, 177.21471, 10.8528)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*.

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Components

#1: Protein BETA-LACTAMASE


Mass: 28433.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / References: UniProt: P00808, beta-lactamase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 579 / 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: 2.36 Å3/Da / Density % sol: 47.81 %
Crystal grow
*PLUS
pH: 6.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.5 mg/mlenzyme 1drop
25 mMpenicillin G1drop
32 mM1dropMgCl2
42 mM1dropNaN3
525 %methoxypolyethyleneglycol1reservoir
625 mMsodium cacodylate-HEPES1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 29095 / Num. measured all: 87548 / Rmerge(I) obs: 0.051

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementHighest resolution: 2 Å / σ(F): 0 /
RfactorNum. reflection
obs0.182 28031
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4000 0 10 579 4589
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.005
X-RAY DIFFRACTIONp_angle_d1.5
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
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_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 10 Å / Num. reflection obs: 28031 / σ(F): 3 / Rfactor all: 0.182 / Rfactor obs: 0.172
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 14.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.014
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.5
X-RAY DIFFRACTIONp_plane_restr0.0270.014
X-RAY DIFFRACTIONp_chiral_restr0.130.111
X-RAY DIFFRACTIONp_scbond_it21.1
X-RAY DIFFRACTIONp_scangle_it31.9

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