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- PDB-2blm: BETA-LACTAMASE OF BACILLUS LICHENIFORMIS 749(SLASH)C AT 2 ANGSTRO... -

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Basic information

Entry
Database: PDB / ID: 2blm
TitleBETA-LACTAMASE OF BACILLUS LICHENIFORMIS 749(SLASH)C AT 2 ANGSTROMS RESOLUTION
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/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsMoews, P.C. / Knox, J.R. / Dideberg, O.
Citation
Journal: Proteins / Year: 1990
Title: Beta-lactamase of Bacillus licheniformis 749/C at 2 A resolution.
Authors: Moews, P.C. / Knox, J.R. / Dideberg, O. / Charlier, P. / Frere, J.M.
#1: Journal: Molecular Recognition. Chemical and Biochemical Problems
Year: 1989
Title: Crystallographic Comparison of Penicillin-Recognizing Enzymes
Authors: Knox, J.R. / Kelly, J.A.
#2: Journal: Science / Year: 1986
Title: On the Origin of Bacterial Resistance to Penicillin. Comparison of a Beta-Lactamase and a Penicillin Target
Authors: Kelly, J.A. / Dideberg, O. / Charlier, P. / Wery, J.P. / Libert, M. / Moews, P.C. / Knox, J.R. / Duez, C. / Fraipont, C. / Joris, B. / Dusart, J. / Frere, J.M. / Ghuysen, J.M.
History
DepositionFeb 2, 1990Processing site: BNL
Revision 1.0Oct 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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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


Theoretical massNumber of molelcules
Total (without water)59,0852
Polymers59,0852
Non-polymers00
Water00
1
A: BETA-LACTAMASE


Theoretical massNumber of molelcules
Total (without water)29,5421
Polymers29,5421
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BETA-LACTAMASE


Theoretical massNumber of molelcules
Total (without water)29,5421
Polymers29,5421
Non-polymers00
Water0
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 / Coordinate model: Cα atoms only


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

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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
pH: 5.5 / Method: vapor diffusion / Details: used macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 %(w/v)PEG60001reservoir
250 mMsodium cacodylate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 6 Å / Num. measured all: 53000 / Rmerge(I) obs: 0.053

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2→10 Å / σ(F): 3 /
RfactorNum. reflection
obs0.208 27330
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms520 0 0 0 520
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.014
X-RAY DIFFRACTIONp_angle_d0.0460.027
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0180.016
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_it4.43
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.210.13
X-RAY DIFFRACTIONp_singtor_nbd0.170.35
X-RAY DIFFRACTIONp_multtor_nbd0.20.35
X-RAY DIFFRACTIONp_xhyhbond_nbd0.180.35
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.52.5
X-RAY DIFFRACTIONp_staggered_tor22.830
X-RAY DIFFRACTIONp_orthonormal_tor24.630
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Rfactor obs: 0.208 / Rfactor Rwork: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS

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