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- PDB-6dd0: Crystal structure of VIM-2 complexed with compound 8 -

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Basic information

Entry
Database: PDB / ID: 6dd0
TitleCrystal structure of VIM-2 complexed with compound 8
ComponentsBeta-lactamase class B VIM-2
KeywordsHYDROLASE / beta-lactamase / carbapenemase / phosphonate / inhibitor
Function / homology
Function and homology information


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 / Chem-P9T / beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsPemberton, O.A. / Chen, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI103158-04 United States
CitationJournal: J.Med.Chem. / Year: 2019
Title: Heteroaryl Phosphonates as Noncovalent Inhibitors of Both Serine- and Metallocarbapenemases.
Authors: Pemberton, O.A. / Jaishankar, P. / Akhtar, A. / Adams, J.L. / Shaw, L.N. / Renslo, A.R. / Chen, Y.
History
DepositionMay 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: 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 1.2Oct 9, 2019Group: Data collection / 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
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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
B: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,56814
Polymers51,3872
Non-polymers1,18112
Water10,106561
1
A: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2847
Polymers25,6931
Non-polymers5906
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2847
Polymers25,6931
Non-polymers5906
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.630, 79.130, 67.790
Angle α, β, γ (deg.)90.000, 130.500, 90.000
Int Tables number5
Space group name H-MC121

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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: 25693.488 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, VIM-2, vim-2
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9K2N0
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-P9T / [(5,7-difluoro-2-oxo-2H-1-benzopyran-4-yl)methyl]phosphonic acid


Mass: 276.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H7F2O5P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 561 / Source method: isolated from a natural source / Formula: H2O

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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: 2.04 Å3/Da / Density % sol: 39.61 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Calcium acetate, 20% (w/v) PEG 3350, 1 mM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→33.89 Å / Num. all: 65885 / Num. obs: 65885 / % possible obs: 100 % / Redundancy: 3.7 % / Biso Wilson estimate: 8.15 Å2 / CC1/2: 0.948 / Rmerge(I) obs: 0.281 / Rpim(I) all: 0.174 / Rrim(I) all: 0.332 / Rsym value: 0.281 / Net I/σ(I): 5.9 / Num. measured all: 241046
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.6 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym value% possible all
1.5-1.581.3296130.1550.0710.1370.116100
4.74-33.890.11621420.9610.0690.1340.11499.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.18 Å31.39 Å
Translation4.18 Å31.39 Å

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Processing

Software
NameVersionClassification
iMOSFLM7.2.1data reduction
SCALA3.3.22data scaling
PHASER2.8.1phasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KO3

1ko3


Resolution: 1.5→31.386 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0.59 / Phase error: 23.7
RfactorNum. reflection% reflection
Rfree0.2253 6299 4.91 %
Rwork0.1831 --
obs0.1852 65884 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 54.24 Å2 / Biso mean: 16.1283 Å2 / Biso min: 2.82 Å2
Refinement stepCycle: final / Resolution: 1.5→31.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3464 0 58 561 4083
Biso mean--19.66 28.28 -
Num. residues----460
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.5170.31142150.26954023423898
1.517-1.53490.33571460.26754049419597
1.5349-1.55360.29991870.25244100428798
1.5536-1.57330.27611600.25964036419698
1.5733-1.5940.33791960.25944079427598
1.594-1.61580.32132340.24213994422898
1.6158-1.63890.28372110.24144031424298
1.6389-1.66340.29791790.23734114429398
1.6634-1.68930.25032020.23234027422999
1.6893-1.7170.2751460.22934121426799
1.717-1.74660.27452390.22034066430599
1.7466-1.77840.27562530.2174005425899
1.7784-1.81260.26582310.20894065429699
1.8126-1.84960.2482190.20824084430399
1.8496-1.88980.26261890.19674061425099
1.8898-1.93380.25322280.19514104433299
1.9338-1.98210.22892710.18784005427699
1.9821-2.03570.21851590.17514115427499
2.0357-2.09560.23052200.17714131435199
2.0956-2.16320.2182240.16844042426699
2.1632-2.24050.22172720.1694045431799
2.2405-2.33020.23041890.16894083427299
2.3302-2.43620.22832100.16464051426199
2.4362-2.56460.20882060.15954090429699
2.5646-2.72520.19123040.15114021432599
2.7252-2.93550.17961760.15864133430999
2.9355-3.23060.22141940.15834106430099
3.2306-3.69740.16723060.14333994430099
3.6974-4.6560.16571910.13854129432099
4.656-31.39270.20511420.16884159430199

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