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- PDB-6op7: Structure of oxidized VIM-20 -

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Basic information

Entry
Database: PDB / ID: 6op7
TitleStructure of oxidized VIM-20
ComponentsMetallo-beta-lactamase VIM-20
KeywordsHYDROLASE / metallo-beta-lactamase
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 speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsPage, R.C. / Shurina, B.A. / Montgomery, J.S. / Orischak, M.G. / Nix, J.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM128595 United States
CitationJournal: Mbio / Year: 2019
Title: A Single Salt Bridge in VIM-20 Increases Protein Stability and Antibiotic Resistance under Low-Zinc Conditions.
Authors: Cheng, Z. / Shurina, B.A. / Bethel, C.R. / Thomas, P.W. / Marshall, S.H. / Thomas, C.A. / Yang, K. / Kimble, R.L. / Montgomery, J.S. / Orischak, M.G. / Miller, C.M. / Tennenbaum, J.L. / Nix, ...Authors: Cheng, Z. / Shurina, B.A. / Bethel, C.R. / Thomas, P.W. / Marshall, S.H. / Thomas, C.A. / Yang, K. / Kimble, R.L. / Montgomery, J.S. / Orischak, M.G. / Miller, C.M. / Tennenbaum, J.L. / Nix, J.C. / Tierney, D.L. / Fast, W. / Bonomo, R.A. / Page, R.C. / Crowder, M.W.
History
DepositionApr 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 1, 2020Group: 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 / struct_conn_type
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.4Nov 15, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / struct_ref
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_ref.pdbx_seq_one_letter_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metallo-beta-lactamase VIM-20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2416
Polymers25,9331
Non-polymers3085
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.860, 77.860, 79.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Metallo-beta-lactamase VIM-20


Mass: 25932.764 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: blaVIM-20 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A344X7M2
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.12 Å3/Da / Density % sol: 38.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.17 M ammonium acetate, 0.085 M Sodium Acetate, 25.5 % (w/v) PEG 4000, and 15 % (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Mar 1, 2019
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.37→39.68 Å / Num. obs: 84110 / % possible obs: 99.9 % / Redundancy: 9.1 % / Biso Wilson estimate: 15.8 Å2 / CC1/2: 0.99 / Net I/σ(I): 19.2
Reflection shellResolution: 1.37→1.42 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4337 / CC1/2: 0.71 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NQ2

4nq2


Resolution: 1.37→39.68 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.57
RfactorNum. reflection% reflectionSelection details
Rfree0.1918 3245 3.86 %Random selection
Rwork0.1625 ---
obs0.1637 84110 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.37→39.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1693 0 14 142 1849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051761
X-RAY DIFFRACTIONf_angle_d0.8072414
X-RAY DIFFRACTIONf_dihedral_angle_d19.054602
X-RAY DIFFRACTIONf_chiral_restr0.079282
X-RAY DIFFRACTIONf_plane_restr0.005316
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.39050.31911380.31793543X-RAY DIFFRACTION100
1.3905-1.41220.32171510.28733501X-RAY DIFFRACTION100
1.4122-1.43530.26361440.27063497X-RAY DIFFRACTION100
1.4353-1.46010.25151410.25273494X-RAY DIFFRACTION100
1.4601-1.48660.27671330.23483561X-RAY DIFFRACTION100
1.4866-1.51520.28961430.22523472X-RAY DIFFRACTION100
1.5152-1.54620.29511330.20143584X-RAY DIFFRACTION100
1.5462-1.57980.26491390.20293493X-RAY DIFFRACTION100
1.5798-1.61650.26921380.18813511X-RAY DIFFRACTION100
1.6165-1.6570.22061480.1763501X-RAY DIFFRACTION100
1.657-1.70180.22581400.15723512X-RAY DIFFRACTION100
1.7018-1.75180.18991390.14623548X-RAY DIFFRACTION100
1.7518-1.80840.19891480.14233468X-RAY DIFFRACTION100
1.8084-1.8730.20691340.13453511X-RAY DIFFRACTION100
1.873-1.9480.15061450.13123526X-RAY DIFFRACTION100
1.948-2.03670.17511410.13143528X-RAY DIFFRACTION100
2.0367-2.1440.18231350.13333502X-RAY DIFFRACTION100
2.144-2.27840.19161460.14313508X-RAY DIFFRACTION100
2.2784-2.45420.18141390.14833531X-RAY DIFFRACTION100
2.4542-2.70120.14891390.14893546X-RAY DIFFRACTION100
2.7012-3.09190.19431430.15513520X-RAY DIFFRACTION100
3.0919-3.89490.1561390.1493484X-RAY DIFFRACTION100
3.8949-39.69660.18381490.17363524X-RAY DIFFRACTION100

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