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- PDB-6dd1: Crystal structure of VIM-2 complexed with compound 14 -

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Basic information

Entry
Database: PDB / ID: 6dd1
TitleCrystal structure of VIM-2 complexed with compound 14
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 / [(quinolin-8-yl)methyl]phosphonic acid / beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 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)52,90816
Polymers51,3872
Non-polymers1,52114
Water10,503583
1
A: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4548
Polymers25,6931
Non-polymers7617
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)26,4548
Polymers25,6931
Non-polymers7617
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.480, 79.200, 77.880
Angle α, β, γ (deg.)90.000, 138.630, 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-M3Q / [(quinolin-8-yl)methyl]phosphonic acid


Mass: 223.165 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H10NO3P / 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.: 583 / 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: 2.03 Å3/Da / Density % sol: 39.48 %
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: 1.7→33.87 Å / Num. all: 45248 / Num. obs: 45248 / % possible obs: 100 % / Redundancy: 3.7 % / Biso Wilson estimate: 10.93 Å2 / CC1/2: 0.981 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.114 / Rrim(I) all: 0.218 / Rsym value: 0.186 / Net I/σ(I): 7.7 / Num. measured all: 167930
Reflection shell

Rpim(I) all: 0.032 / Diffraction-ID: 1 / Redundancy: 3.7 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allRsym value% possible all
1.7-1.790.94765890.3420.0630.054100
5.38-33.870.05414700.9960.0610.05399.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.2 Å31.39 Å
Translation4.2 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: 1.7→31.386 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.08 / Phase error: 21.24
RfactorNum. reflection% reflection
Rfree0.2164 4138 4.66 %
Rwork0.1518 --
obs0.1548 45246 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 70.91 Å2 / Biso mean: 18.1417 Å2 / Biso min: 2.98 Å2
Refinement stepCycle: final / Resolution: 1.7→31.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3486 0 82 583 4151
Biso mean--18.32 30.95 -
Num. residues----462
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 (%)
1.7-1.71930.32451340.25992798293299
1.7193-1.73960.2851320.24862815294799
1.7396-1.76080.30951350.24632815295099
1.7608-1.78310.33751930.25282708290199
1.7831-1.80650.2931530.24622807296099
1.8065-1.83130.31441000.23442875297599
1.8313-1.85740.28861390.21662809294899
1.8574-1.88510.27131390.21632790292999
1.8851-1.91460.29091360.20452861299799
1.9146-1.9460.27951500.206227502900100
1.946-1.97950.221090.190728692978100
1.9795-2.01550.22811000.172528362936100
2.0155-2.05430.26661540.169828513005100
2.0543-2.09620.22341040.157828862990100
2.0962-2.14180.20631150.153127882903100
2.1418-2.19160.2131710.156228102981100
2.1916-2.24640.23391790.149827682947100
2.2464-2.30710.20321770.148128293006100
2.3071-2.3750.20361590.142827512910100
2.375-2.45160.22971770.134728092986100
2.4516-2.53920.19561460.139528372983100
2.5392-2.64080.1966830.128328862969100
2.6408-2.76090.21111400.127627802920100
2.7609-2.90640.2051200.1328702990100
2.9064-3.08830.24211640.126928623026100
3.0883-3.32650.1563940.116128132907100
3.3265-3.66080.13531520.104628252977100
3.6608-4.18950.15641200.105928462966100
4.1895-5.27420.18011490.104628342983100
5.2742-31.39150.17791140.152528602974100

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