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- PDB-8i52: Crystal structure of VIM-2 metallo-beta-lactamase in complex with... -

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Basic information

Entry
Database: PDB / ID: 8i52
TitleCrystal structure of VIM-2 metallo-beta-lactamase in complex with 10-HHIA
ComponentsBeta-lactamase class B VIM-2
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 / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
FORMIC ACID / (2~{S})-2-butyl-3-methylidene-butanedioic acid / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsWachino, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of VIM-2 Metallo-beta-lactamase in complex with 10-HHIA
Authors: Wachino, J.
History
DepositionJan 23, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase class B VIM-2
D: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,04713
Polymers52,2842
Non-polymers76311
Water10,845602
1
A: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4306
Polymers26,1421
Non-polymers2885
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6167
Polymers26,1421
Non-polymers4746
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.320, 79.250, 67.900
Angle α, β, γ (deg.)90.000, 130.140, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-453-

HOH

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Components

#1: Protein Beta-lactamase class B VIM-2 / BlaVIM-2 / Metallo beta-lactamase / Metallo-beta lactamase protein / Metallo-beta-lactamase VIM-2 / ...BlaVIM-2 / Metallo beta-lactamase / Metallo-beta lactamase protein / Metallo-beta-lactamase VIM-2 / VIM-2 / VIM-2 beta-lactamase / VIM-2 class B metallo b-lactamase / VIM-2 metallo-beta-lactamase / VIM-2 type metallo-beta-lactamase


Mass: 26142.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: blaVIM-2, bla vim-2, bla-VIM-2, blasVIM-2, blaVIM2, blm, VIM-2, vim-2, PAERUG_P32_London_17_VIM_2_10_11_06255
Production host: Escherichia coli (E. coli) / References: UniProt: Q9K2N0, beta-lactamase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-OR6 / (2~{S})-2-butyl-3-methylidene-butanedioic acid


Mass: 186.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C9H14O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 602 / 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: 2.11 Å3/Da / Density % sol: 41.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M Magnesium formate dehydrate, 25% PEG 3350

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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 PILATUS3 6M / Detector: PIXEL / Date: Mar 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→55.393 Å / Num. obs: 55926 / % possible obs: 99.7 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.034 / Rrim(I) all: 0.089 / Net I/σ(I): 16
Reflection shellResolution: 1.58→1.67 Å / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 8 / Num. unique obs: 8043 / Rpim(I) all: 0.084 / Rrim(I) all: 0.221

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YD7

5yd7


Resolution: 1.58→55.393 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.188 / WRfactor Rwork: 0.156 / SU B: 1.316 / SU ML: 0.048 / Average fsc free: 0.9795 / Average fsc work: 0.9864 / Cross valid method: FREE R-VALUE / ESU R: 0.082 / ESU R Free: 0.081
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1784 2909 5.202 %
Rwork0.1474 53016 -
all0.149 --
obs-55925 99.576 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 11.261 Å2
Baniso -1Baniso -2Baniso -3
1-0.028 Å20 Å2-0.105 Å2
2--0.158 Å20 Å2
3----0.004 Å2
Refinement stepCycle: LAST / Resolution: 1.58→55.393 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3486 0 31 602 4119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0123758
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163322
X-RAY DIFFRACTIONr_angle_refined_deg1.7351.6565142
X-RAY DIFFRACTIONr_angle_other_deg0.5831.5677740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5515491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.682525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.20210548
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.58110164
X-RAY DIFFRACTIONr_chiral_restr0.0850.2579
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024443
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02739
X-RAY DIFFRACTIONr_nbd_refined0.220.2632
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.23086
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21784
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21966
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2402
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other00.21
X-RAY DIFFRACTIONr_metal_ion_refined0.9360.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2320.211
X-RAY DIFFRACTIONr_nbd_other0.1550.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1630.249
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0280.21
X-RAY DIFFRACTIONr_mcbond_it1.1761.1131925
X-RAY DIFFRACTIONr_mcbond_other1.1761.1141926
X-RAY DIFFRACTIONr_mcangle_it1.7821.6682429
X-RAY DIFFRACTIONr_mcangle_other1.7821.6682430
X-RAY DIFFRACTIONr_scbond_it2.11.3241833
X-RAY DIFFRACTIONr_scbond_other2.0991.3241834
X-RAY DIFFRACTIONr_scangle_it3.1011.9052713
X-RAY DIFFRACTIONr_scangle_other3.11.9052714
X-RAY DIFFRACTIONr_lrange_it4.67619.9744212
X-RAY DIFFRACTIONr_lrange_other4.5519.3584130
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
1.58-1.6210.1962340.16138320.16341250.9750.98498.56970.145
1.621-1.6650.2032630.15537090.15840130.9760.98598.97830.14
1.665-1.7140.1842300.15336610.15539240.980.98599.1590.141
1.714-1.7660.1741950.14536080.14738300.9810.98799.2950.136
1.766-1.8240.1771790.14934900.15136910.9810.98699.4040.142
1.824-1.8880.1961770.1533950.15235920.9770.98699.44320.146
1.888-1.9590.1771800.15632120.15734060.980.98599.5890.153
1.959-2.0390.1851320.15432010.15533430.9770.98599.70090.156
2.039-2.130.171830.1530020.15131910.9820.98699.8120.155
2.13-2.2340.2011770.1528310.15330120.9760.98699.86720.156
2.234-2.3540.1771350.1427970.14229340.9810.98899.93180.15
2.354-2.4970.1821310.14226190.14427500.980.9881000.156
2.497-2.6690.1911330.1424390.14325720.9740.9881000.154
2.669-2.8820.1831580.14422410.14723990.9820.9871000.164
2.882-3.1560.147850.14221530.14222380.9860.9881000.16
3.156-3.5270.163890.1519010.1519900.9840.9881000.17
3.527-4.070.141810.13817050.13817860.9880.9891000.163
4.07-4.9780.144500.13214650.13215150.9870.9911000.166
4.978-7.0120.242530.16711180.1711710.9850.9871000.2
7.012-55.3930.198440.1686360.176800.9830.9791000.209

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