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- PDB-6o5t: Crystal Structure of VIM-2 with Compound 16 -

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Basic information

Entry
Database: PDB / ID: 6o5t
TitleCrystal Structure of VIM-2 with Compound 16
ComponentsBeta-lactamase class B VIM-2
KeywordsHYDROLASE/INHIBITOR / Carbapenemase / Phosphonate / inhibitor / complex / HYDROLASE / HYDROLASE-INHIBITOR complex
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-L8J / beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAkhtar, A. / Chen, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)Al103158 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
DepositionMar 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 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 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _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)53,11719
Polymers51,3872
Non-polymers1,73017
Water3,459192
1
A: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5299
Polymers25,6931
Non-polymers8368
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,58810
Polymers25,6931
Non-polymers8959
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.389, 79.185, 67.501
Angle α, β, γ (deg.)90.000, 130.600, 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.: 8
Source method: isolated from a genetically manipulated source
Formula: Zn
#3: Chemical ChemComp-L8J / [(5,7-dibromo-2-oxo-1,2-dihydroquinolin-4-yl)methyl]phosphonic acid


Mass: 396.957 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H8Br2NO4P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.08 Å3/Da / Density % sol: 40.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M Calcium Acetate, 20%(w/v) PEG-3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 23884 / % possible obs: 99.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.052 / Rrim(I) all: 0.101 / Χ2: 0.628 / Net I/σ(I): 5.2 / Num. measured all: 88997
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.143.10.32911120.840.2130.3940.43895
2.14-2.183.30.31611930.8660.2010.3750.4297.4
2.18-2.223.40.3111640.8910.1940.3660.42799.1
2.22-2.263.60.31111890.9110.1920.3670.41999.7
2.26-2.313.80.26712000.9270.1610.3120.41599.9
2.31-2.373.80.24111850.9390.1450.2820.44100
2.37-2.423.80.22411970.9510.1340.2620.451100
2.42-2.493.80.19812130.9540.1180.230.472100
2.49-2.563.80.1911680.9560.1130.2220.473100
2.56-2.653.80.16211930.9750.0960.1890.512100
2.65-2.743.80.14112100.9780.0840.1650.515100
2.74-2.853.80.12311920.9850.0730.1440.558100
2.85-2.983.80.1112040.9830.0660.1290.59100
2.98-3.143.80.09411910.990.0560.110.672100
3.14-3.333.80.07911940.9910.0470.0920.818100
3.33-3.593.80.06412250.9950.0380.0750.862100
3.59-3.953.80.05511840.9950.0330.0650.851100
3.95-4.523.80.0512050.9960.0290.0580.944100
4.52-5.73.80.04712220.9970.0280.0550.951100
5.7-503.80.04712430.9970.0280.0551.15499.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3228refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4bz3

4bz3


Resolution: 2.1→39.593 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 24.57
RfactorNum. reflection% reflection
Rfree0.236 2029 8.5 %
Rwork0.1789 --
obs0.1838 23880 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.91 Å2 / Biso mean: 28.9246 Å2 / Biso min: 9.65 Å2
Refinement stepCycle: final / Resolution: 2.1→39.593 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3506 0 85 192 3783
Biso mean--44.25 31.67 -
Num. residues----466
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0975-2.14990.27551350.19871442157793
2.1499-2.2080.30121410.20481524166598
2.208-2.2730.29931460.211315681714100
2.273-2.34640.26411450.198215491694100
2.3464-2.43020.24621460.196315771723100
2.4302-2.52750.27571410.194515581699100
2.5275-2.64250.27141510.195915651716100
2.6425-2.78180.27591420.196815701712100
2.7818-2.9560.2491500.186615901740100
2.956-3.18420.25131420.190215461688100
3.1842-3.50440.20371500.173115721722100
3.5044-4.01110.23871440.162715931737100
4.0111-5.05190.19231470.14415801727100
5.0519-39.59950.19721490.17516171766100

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