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- PDB-7uyd: Inhibitor bound VIM1 -

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Basic information

Entry
Database: PDB / ID: 7uyd
TitleInhibitor bound VIM1
ComponentsMetallo-beta-lactamase VIM-2-like protein
KeywordsHYDROLASE
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
ACETATE ION / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1 Å
AuthorsFischmann, T.O. / Scapin, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2024
Title: Structure Guided Discovery of Novel Pan Metallo-beta-Lactamase Inhibitors with Improved Gram-Negative Bacterial Cell Penetration.
Authors: Dong, S. / Zhao, Z. / Tang, H. / Li, G. / Pan, J. / Gu, X. / Jiang, J. / Xiao, L. / Scapin, G. / Hunter, D.N. / Yang, D. / Huang, Y. / Bennett, F. / Yang, S.W. / Mandal, M. / Tang, H. / Su, ...Authors: Dong, S. / Zhao, Z. / Tang, H. / Li, G. / Pan, J. / Gu, X. / Jiang, J. / Xiao, L. / Scapin, G. / Hunter, D.N. / Yang, D. / Huang, Y. / Bennett, F. / Yang, S.W. / Mandal, M. / Tang, H. / Su, J. / Tudge, C. / deJesus, R.K. / Ding, F.X. / Lombardo, M. / Hicks, J.D. / Fischmann, T. / Mirza, A. / Dayananth, P. / Painter, R.E. / Villafania, A. / Garlisi, C.G. / Zhang, R. / Mayhood, T.W. / Si, Q. / Li, N. / Amin, R.P. / Bhatt, B. / Chen, F. / Regan, C.P. / Regan, H. / Lin, X. / Wu, J. / Leithead, A. / Pollack, S.R. / Scott, J.D. / Nargund, R.P. / Therien, A.G. / Black, T. / Young, K. / Pasternak, A.
History
DepositionMay 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metallo-beta-lactamase VIM-2-like protein
B: Metallo-beta-lactamase VIM-2-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,17822
Polymers50,9352
Non-polymers1,24320
Water11,602644
1
A: Metallo-beta-lactamase VIM-2-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,08911
Polymers25,4671
Non-polymers62210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metallo-beta-lactamase VIM-2-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,08911
Polymers25,4671
Non-polymers62210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.652, 78.957, 67.764
Angle α, β, γ (deg.)90.000, 130.520, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Metallo-beta-lactamase VIM-2-like protein


Mass: 25467.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaVIM / Production host: Escherichia coli (E. coli) / References: UniProt: B8QIQ9
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 644 / 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: 2.05 Å3/Da / Density % sol: 39.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 0.3 M Ammonium acetate 0.1 M Tris hydrochloride pH 7.6 25.0 w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1→55.5 Å / Num. obs: 217945 / % possible obs: 98 % / Redundancy: 3.2 % / Biso Wilson estimate: 7.21 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.031 / Rrim(I) all: 0.058 / Net I/σ(I): 15.2 / Num. measured all: 701529
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1-1.072.90.361109969380360.8440.2460.4383.194.6
2.82-55.53.20.0353198098470.9970.0220.04242.698.7

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.3.6data scaling
BUSTER2.11.5refinement
PDB_EXTRACT3.27data extraction
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1→14.64 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.9629 / SU R Cruickshank DPI: 0.022 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.023 / SU Rfree Blow DPI: 0.024 / SU Rfree Cruickshank DPI: 0.023
RfactorNum. reflection% reflectionSelection details
Rfree0.1605 10810 5 %RANDOM
Rwork0.1473 ---
obs0.1479 216180 97.99 %-
Displacement parametersBiso max: 79.65 Å2 / Biso mean: 13.73 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--1.2708 Å20 Å20.3984 Å2
2--1.4498 Å20 Å2
3----0.179 Å2
Refine analyzeLuzzati coordinate error obs: 0.1 Å
Refinement stepCycle: final / Resolution: 1→14.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3473 0 62 659 4194
Biso mean--15.22 26.15 -
Num. residues----464
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1209SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes81HARMONIC2
X-RAY DIFFRACTIONt_gen_planes574HARMONIC5
X-RAY DIFFRACTIONt_it3684HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion491SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4908SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3684HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5044HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion5.3
X-RAY DIFFRACTIONt_other_torsion14.08
LS refinement shellResolution: 1→1.03 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2256 799 5.29 %
Rwork0.2021 14309 -
all0.2034 15108 -
obs--97.99 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.37930.12540.09560.64260.25260.4898-0.00810.01230.0187-0.0448-0.02450.0482-0.0123-0.0370.0326-0.02270.0011-0.0021-0.01050.0002-0.027824.0903-9.94990.1959
20.4439-0.09010.22270.4735-0.19180.56480.00570.0209-0.02570.00970.0050.0296-0.0003-0.0123-0.0108-0.02390.00020.0048-0.01150.0014-0.0243.283310.507223.8212
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A32 - 263
2X-RAY DIFFRACTION2{ B|* }B32 - 263

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