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- PDB-7uya: Inhibitor bound VIM1 -

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Basic information

Entry
Database: PDB / ID: 7uya
TitleInhibitor bound VIM1
ComponentsBeta-lactamase VIM-1
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
Chem-OKC / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.01 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

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Assembly

Deposited unit
A: Beta-lactamase VIM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5254
Polymers26,0101
Non-polymers5153
Water4,792266
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.530, 67.565, 40.102
Angle α, β, γ (deg.)90.000, 91.660, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase VIM-1 / Class B carbapenemase VIM-1 / Metallo-beta-lactamase / Metallo-beta-lactamase VIM-1 / Metallobeta- ...Class B carbapenemase VIM-1 / Metallo-beta-lactamase / Metallo-beta-lactamase VIM-1 / Metallobeta-lactamase / Subclass B1 metallo-beta-lactamase VIM-1 / VIM-1 / VIM-1 metallo-beta-lactamase / VIM-1 protein


Mass: 26009.799 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaVIM, blaVIM-1, CAZ10_38240, CAZ10_38245 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9XAY4
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-OKC / (2M)-4'-(piperidin-4-yl)-2-(1H-tetrazol-5-yl)[1,1'-biphenyl]-3-sulfonamide


Mass: 384.455 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20N6O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.06 Å3/Da / Density % sol: 40.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Magnesium chloride 0.1 M Tris hydrochloride pH 8.5 30.0 w/v polyethylene glycol 4000

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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 PILATUS3 6M / Detector: PIXEL / Date: Jun 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.01→67.57 Å / Num. obs: 104663 / % possible obs: 94.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 9.14 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.029 / Rrim(I) all: 0.054 / Net I/σ(I): 16.1 / Num. measured all: 344796
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
1.01-1.043.10.5082797791510.7350.3380.612290.1
4.04-67.573.30.047558916870.9850.0310.05740.495.1

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.1.27data scaling
BUSTER2.11.4refinement
PDB_EXTRACT3.27data extraction
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.01→14.79 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.9633 / SU R Cruickshank DPI: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.026 / SU Rfree Blow DPI: 0.026 / SU Rfree Cruickshank DPI: 0.026
RfactorNum. reflection% reflectionSelection details
Rfree0.1786 5195 4.98 %RANDOM
Rwork0.1658 ---
obs0.1664 104402 94.9 %-
Displacement parametersBiso max: 82.79 Å2 / Biso mean: 15.64 Å2 / Biso min: 6.85 Å2
Baniso -1Baniso -2Baniso -3
1--1.1446 Å20 Å20.2498 Å2
2---0.0148 Å20 Å2
3---1.1593 Å2
Refine analyzeLuzzati coordinate error obs: 0.115 Å
Refinement stepCycle: final / Resolution: 1.01→14.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1716 0 29 266 2011
Biso mean--12.42 26.7 -
Num. residues----230
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d617SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes46HARMONIC2
X-RAY DIFFRACTIONt_gen_planes297HARMONIC5
X-RAY DIFFRACTIONt_it1857HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion244SEMIHARMONIC5
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_contact2412SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1857HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2564HARMONIC21.12
X-RAY DIFFRACTIONt_omega_torsion5.07
X-RAY DIFFRACTIONt_other_torsion15.97
LS refinement shellResolution: 1.01→1.04 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2188 352 4.82 %
Rwork0.2207 6951 -
all0.2206 7303 -
obs--94.9 %
Refinement TLS params.Method: refined / Origin x: -17.0172 Å / Origin y: -2.49 Å / Origin z: -5.457 Å
111213212223313233
T-0.0457 Å2-0.0065 Å20.0053 Å2--0.0234 Å2-0.0011 Å2---0.0206 Å2
L0.7239 °2-0.2339 °2-0.1038 °2-0.6933 °20.0488 °2--0.7684 °2
S-0.0098 Å °-0.002 Å °0.0349 Å °-0.0338 Å °0.0121 Å °-0.0461 Å °-0.0039 Å °0.0257 Å °-0.0023 Å °
Refinement TLS groupSelection details: { A|* }

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