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- PDB-7ev5: Crystal structure of BLEG-1 B3 metallo-beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 7ev5
TitleCrystal structure of BLEG-1 B3 metallo-beta-lactamase
ComponentsLactamase_B domain-containing protein
KeywordsHYDROLASE / B3 metallo-beta-lactamase / glyoxalase II / Metallo-hydrolase-like_MBL-fold protein
Function / homology: / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / metal ion binding / IODIDE ION / Metallo-beta-lactamase domain-containing protein
Function and homology information
Biological speciesBacillus lehensis G1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsAu, S.X. / Muhd Noor, N.D. / Matsumura, H. / Rahman, R.N.Z.R.A. / Normi, Y.M.
CitationJournal: Int J Mol Sci / Year: 2021
Title: Dual Activity BLEG-1 from Bacillus lehensis G1 Revealed Structural Resemblance to B3 Metallo-beta-Lactamase and Glyoxalase II: An Insight into Its Enzyme Promiscuity and Evolutionary Divergence.
Authors: Au, S.X. / Dzulkifly, N.S. / Muhd Noor, N.D. / Matsumura, H. / Raja Abdul Rahman, R.N.Z. / Normi, Y.M.
History
DepositionMay 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lactamase_B domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,65113
Polymers23,2511
Non-polymers1,40012
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-78 kcal/mol
Surface area9260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.356, 55.356, 143.094
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Lactamase_B domain-containing protein / BLEG-1


Mass: 23251.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus lehensis G1 (bacteria) / Plasmid: pET-28(b) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A060M4R1
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47 % / Description: Tetragonal
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: NaI, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: CCD / Date: Jul 19, 2019
RadiationMonochromator: Copper / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.44→50 Å / Num. obs: 40528 / % possible obs: 98 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 28.5
Reflection shellResolution: 1.44→1.46 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 4 / Num. unique obs: 1991 / CC1/2: 0.899 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX1.16_3549-000refinement
PHENIX1.16_3549-000phasing
HKL-3000v714ndata reduction
HKL-3000v714ndata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XF4

2xf4


Resolution: 1.44→30.26 Å / Cross valid method: FREE R-VALUE / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2085 2087 5.16 %
Rwork0.1844 --
obs0.1856 40457 98 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.3 Å2
Refinement stepCycle: LAST / Resolution: 1.44→30.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1632 0 12 244 1888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051723
X-RAY DIFFRACTIONf_angle_d0.8042360
X-RAY DIFFRACTIONf_dihedral_angle_d3.085994
X-RAY DIFFRACTIONf_chiral_restr0.088269
X-RAY DIFFRACTIONf_plane_restr0.006306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.490.25321950.23433772X-RAY DIFFRACTION98
1.49-1.550.25062290.19813808X-RAY DIFFRACTION100
1.55-1.620.21392170.19153817X-RAY DIFFRACTION100
1.62-1.710.22251830.18553819X-RAY DIFFRACTION99
1.71-1.810.22641940.18523777X-RAY DIFFRACTION98
1.81-1.950.20322070.1963752X-RAY DIFFRACTION97
1.95-2.150.19651940.18543768X-RAY DIFFRACTION96
2.15-2.460.24052270.18793712X-RAY DIFFRACTION95
2.46-3.10.18972190.19153956X-RAY DIFFRACTION99
3.1-30.260.19312220.16664189X-RAY DIFFRACTION99

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