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- PDB-4blm: BETA-LACTAMASE OF BACILLUS LICHENIFORMIS 749(SLASH)C. REFINEMENT ... -

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Basic information

Entry
Database: PDB / ID: 4blm
TitleBETA-LACTAMASE OF BACILLUS LICHENIFORMIS 749(SLASH)C. REFINEMENT AT 2 ANGSTROMS RESOLUTION AND ANALYSIS OF HYDRATION
ComponentsBETA-LACTAMASE
KeywordsHYDROLASE(ACTING IN CYCLIC AMIDES)
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: J.Mol.Biol. / Year: 1991
Title: Beta-lactamase of Bacillus licheniformis 749/C. Refinement at 2 A resolution and analysis of hydration.
Authors: Knox, J.R. / Moews, P.C.
#1: Journal: Proteins / Year: 1990
Title: Beta-Lactamase of Bacillus Licheniformis 749(Slash)C at 2 Angstroms Resolution
Authors: Moews, P.C. / Knox, J.R. / Dideberg, O. / Charlier, P. / Frere, J.-M.
History
DepositionMay 28, 1991Processing site: BNL
Revision 1.0Jan 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 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_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_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)59,2774
Polymers59,0852
Non-polymers1922
Water8,719484
1
A: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6382
Polymers29,5421
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6382
Polymers29,5421
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.800, 90.700, 43.600
Angle α, β, γ (deg.)90.00, 104.50, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUES PRO A 167 AND PRO B 167 ARE CIS PROLINES.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.8708, 0.00104, 0.49164), (0.0011, -1, 0.00018), (0.49164, 0.00039, -0.8708)
Vector: 17.6699, 91.0226, 26.8343)

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Components

#1: Protein BETA-LACTAMASE


Mass: 29542.436 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.: 484 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE NUMBERING IS BASED ON R.P.AMBLER ET AL. (BIOCHEM. J., V. 276, P. 269, 1991). THEREFORE, ...RESIDUE NUMBERING IS BASED ON R.P.AMBLER ET AL. (BIOCHEM. J., V. 276, P. 269, 1991). THEREFORE, THERE ARE NO RESIDUES NUMBERED 58, 84, 85, 239, AND 253.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.15 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.8 / Method: vapor diffusion, hanging drop / Details: Kelly, J. A., (1985) J. Biol. Chem., 260, 6449.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlenzyme1drop
220 %PEG80001reservoir
315 %(w/v)PEG80001drop
450 mMphosphate1droppH6.8

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Data collection

Reflection
*PLUS
Num. all: 30090 / % possible obs: 94 %

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2→10 Å / σ(F): 3 /
RfactorNum. reflection
obs0.161 30090
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4008 0 10 484 4502
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.014
X-RAY DIFFRACTIONp_angle_d0.0360.027
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0180.013
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.61.5
X-RAY DIFFRACTIONp_mcangle_it2.32
X-RAY DIFFRACTIONp_scbond_it32
X-RAY DIFFRACTIONp_scangle_it4.63
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.210.13
X-RAY DIFFRACTIONp_singtor_nbd0.170.35
X-RAY DIFFRACTIONp_multtor_nbd0.230.35
X-RAY DIFFRACTIONp_xhyhbond_nbd0.280.35
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.62.5
X-RAY DIFFRACTIONp_staggered_tor22.230
X-RAY DIFFRACTIONp_orthonormal_tor22.730
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.161
Solvent computation
*PLUS
Displacement parameters
*PLUS

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