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- PDB-7fct: Crystal structure of metallo-beta-lactamase MBLBt2 -

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Basic information

Entry
Database: PDB / ID: 7fct
TitleCrystal structure of metallo-beta-lactamase MBLBt2
ComponentsMetal beta-lactamase
KeywordsCYTOSOLIC PROTEIN / metallo-beta-lactamase / phage
Function / homologyBeta-lactamase superfamily domain / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metal beta-lactamase
Function and homology information
Biological speciesBacillus phage vB_BtM_BMBsp2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.8 Å
AuthorsZhao, F. / Peng, D.H. / Zou, T.T.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31700156 China
National Natural Science Foundation of China (NSFC)31370002 China
CitationJournal: To Be Published
Title: Crystal structure of metallo-beta-lactamase MBLBt2
Authors: Zhao, F. / Peng, D.H. / Zou, T.T.
History
DepositionJul 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metal beta-lactamase
B: Metal beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4099
Polymers56,8192
Non-polymers5907
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-210 kcal/mol
Surface area18860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.561, 153.561, 53.257
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Metal beta-lactamase


Mass: 28409.396 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage vB_BtM_BMBsp2 (virus) / Gene: MBLBt2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A4Y1LJC5
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 3.19 Å3/Da / Density % sol: 62.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 30% MPD, 0.1 M Imidazole pH 7.4, 0.2 M MgCl2, 0.2 M Sodium chloride

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→45 Å / Num. obs: 269158 / % possible obs: 100 % / Redundancy: 14.09 % / Biso Wilson estimate: 15.27 Å2 / CC1/2: 0.99 / Net I/σ(I): 7.56
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 14.6 % / Num. unique obs: 17214 / CC1/2: 0.93 / Rrim(I) all: 0.5 / % possible all: 92.5

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Processing

Software
NameVersionClassification
PHENIX1.19rc5_4047refinement
Cootmodel building
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.8→43.76 Å / SU ML: 0.1385 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.2807
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1859 2000 2.99 %
Rwork0.1617 64795 -
obs0.1624 66795 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.45 Å2
Refinement stepCycle: LAST / Resolution: 1.8→43.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3866 0 26 229 4121
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01043977
X-RAY DIFFRACTIONf_angle_d1.11435364
X-RAY DIFFRACTIONf_chiral_restr0.0787560
X-RAY DIFFRACTIONf_plane_restr0.0078693
X-RAY DIFFRACTIONf_dihedral_angle_d14.19751457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.20121460.18224607X-RAY DIFFRACTION99.96
1.85-1.890.19371400.16644572X-RAY DIFFRACTION99.94
1.89-1.950.19851460.16274583X-RAY DIFFRACTION99.98
1.95-2.010.20351430.16434583X-RAY DIFFRACTION100
2.01-2.090.19971380.16814606X-RAY DIFFRACTION99.94
2.09-2.170.18331410.15744627X-RAY DIFFRACTION100
2.17-2.270.17881390.16834581X-RAY DIFFRACTION100
2.27-2.390.17951430.1674637X-RAY DIFFRACTION100
2.39-2.540.21181460.17854627X-RAY DIFFRACTION100
2.54-2.730.19111410.17774593X-RAY DIFFRACTION100
2.73-3.010.19481430.17464667X-RAY DIFFRACTION100
3.01-3.440.19831430.15834635X-RAY DIFFRACTION100
3.44-4.340.15861420.14324682X-RAY DIFFRACTION100
4.34-4.760.16931490.14874795X-RAY DIFFRACTION99.86

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