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- PDB-7yrp: Crystal structure of VIM-28 metallo-beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 7yrp
TitleCrystal structure of VIM-28 metallo-beta-lactamase
ComponentsMetallo-beta-lactamase VIM-28
KeywordsHYDROLASE / beta-lactamase
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding
Similarity search - Function
: / : / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsShimizu-Ibuka, A. / Sato, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of VIM-28 metallo-beta-lactamase
Authors: Shimizu-Ibuka, A. / Sato, H.
History
DepositionAug 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 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: Metallo-beta-lactamase VIM-28
B: Metallo-beta-lactamase VIM-28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,42614
Polymers52,2342
Non-polymers1,19212
Water4,396244
1
A: Metallo-beta-lactamase VIM-28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8058
Polymers26,1171
Non-polymers6887
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metallo-beta-lactamase VIM-28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6216
Polymers26,1171
Non-polymers5045
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.360, 45.910, 103.260
Angle α, β, γ (deg.)90.000, 103.590, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Metallo-beta-lactamase VIM-28


Mass: 26117.021 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaVIM-28 / Production host: Escherichia coli (E. coli) / References: UniProt: F8UTU0
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.86 Å3/Da / Density % sol: 56.95 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.4 M ammonium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→67.73 Å / Num. obs: 43247 / % possible obs: 99.66 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 8.3
Reflection shellResolution: 2→2.11 Å / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 6128

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WHG

2whg


Resolution: 2→63.483 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.596 / SU ML: 0.097 / Cross valid method: FREE R-VALUE / ESU R: 0.131 / ESU R Free: 0.125
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2037 2147 4.965 %
Rwork0.1718 41098 -
all0.173 --
obs-43245 99.677 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 29.233 Å2
Baniso -1Baniso -2Baniso -3
1--0.001 Å20 Å20.002 Å2
2--0.002 Å20 Å2
3----0.001 Å2
Refinement stepCycle: LAST / Resolution: 2→63.483 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3389 0 66 244 3699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0123527
X-RAY DIFFRACTIONr_bond_other_d0.0440.0163171
X-RAY DIFFRACTIONr_angle_refined_deg1.391.6424823
X-RAY DIFFRACTIONr_angle_other_deg0.9681.5597375
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9735455
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.11520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.13510502
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.50910150
X-RAY DIFFRACTIONr_chiral_restr0.0660.2559
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024077
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02659
X-RAY DIFFRACTIONr_nbd_refined0.2090.2618
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.22688
X-RAY DIFFRACTIONr_nbtor_refined0.1670.21705
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21824
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2247
X-RAY DIFFRACTIONr_metal_ion_refined0.0830.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3940.22
X-RAY DIFFRACTIONr_nbd_other0.1750.229
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1730.218
X-RAY DIFFRACTIONr_mcbond_it2.2063.0031814
X-RAY DIFFRACTIONr_mcbond_other2.2063.0031814
X-RAY DIFFRACTIONr_mcangle_it3.1444.4812265
X-RAY DIFFRACTIONr_mcangle_other3.1444.4852266
X-RAY DIFFRACTIONr_scbond_it3.0563.3761713
X-RAY DIFFRACTIONr_scbond_other3.0553.3771714
X-RAY DIFFRACTIONr_scangle_it4.694.9142556
X-RAY DIFFRACTIONr_scangle_other4.6894.9152557
X-RAY DIFFRACTIONr_lrange_it6.64638.9273828
X-RAY DIFFRACTIONr_lrange_other6.52437.5733767
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2-2.0520.2761430.25729910.25831480.9450.95499.55530.232
2.052-2.1080.2661550.23429260.23630900.9490.96399.70870.212
2.108-2.1690.2091590.22628700.22530420.9690.96699.57260.2
2.169-2.2360.241530.21927380.2229160.9590.96899.14270.191
2.236-2.3090.231480.20126770.20228280.9660.97499.89390.174
2.309-2.390.2431450.19526180.19727730.9640.97699.63940.166
2.39-2.480.2461200.18325030.18626260.9640.97899.88580.158
2.48-2.5810.2251090.17124750.17425850.9710.98299.96130.149
2.581-2.6960.211230.17823290.17924630.9670.9899.55340.155
2.696-2.8270.2111100.17322430.17423630.970.98199.57680.151
2.827-2.980.274870.1720890.17422040.9640.98298.72960.154
2.98-3.160.2251050.15820130.16121270.9720.98499.57690.144
3.16-3.3780.1781090.15718960.15820060.9780.98599.95010.148
3.378-3.6470.1651110.15117580.15218690.9810.9861000.144
3.647-3.9940.159930.14616140.14717070.9850.9871000.144
3.994-4.4630.176750.13514960.13715710.980.9891000.137
4.463-5.150.153720.13113400.13214120.9880.991000.137
5.15-6.2970.189530.16411140.16511670.9830.9861000.164
6.297-8.8610.193480.1548890.1569370.9840.9861000.159
8.861-63.4830.193290.1685180.1695480.9790.9899.81750.196

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