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- PDB-4bz3: Crystal structure of the metallo-beta-lactamase VIM-2 -

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Basic information

Entry
Database: PDB / ID: 4bz3
TitleCrystal structure of the metallo-beta-lactamase VIM-2
ComponentsBETA-LACTAMASE VIM-2
KeywordsHYDROLASE / HYDROLASES / MBL / ANTIBIOTIC RESISTANCE.
Function / homology
Function and homology information


beta-lactamase / hydrolase activity / metal ion binding
Similarity search - Function
: / : / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / beta-lactamase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.294 Å
AuthorsZollman, D. / Brem, J. / McDonough, M.A. / van Berkel, S.S. / Schofield, C.J.
CitationJournal: Antimicrob. Agents Chemother. / Year: 2015
Title: Structural Basis of Metallo-beta-Lactamase Inhibition by Captopril Stereoisomers.
Authors: Brem, J. / van Berkel, S.S. / Zollman, D. / Lee, S.Y. / Gileadi, O. / McHugh, P.J. / Walsh, T.R. / McDonough, M.A. / Schofield, C.J.
History
DepositionJul 23, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Other / Structure summary
Revision 1.2Nov 25, 2015Group: Database references
Revision 1.3Jan 13, 2016Group: Database references
Revision 1.4Feb 21, 2018Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.title / _citation_author.name
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _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.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.ptnr1_symmetry / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-LACTAMASE VIM-2
B: BETA-LACTAMASE VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,05615
Polymers51,3872
Non-polymers66913
Water8,953497
1
A: BETA-LACTAMASE VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0518
Polymers25,6931
Non-polymers3577
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BETA-LACTAMASE VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0057
Polymers25,6931
Non-polymers3116
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.955, 79.689, 68.171
Angle α, β, γ (deg.)90.00, 130.56, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein BETA-LACTAMASE VIM-2 / VIM-2


Mass: 25693.488 Da / Num. of mol.: 2 / Fragment: RESIDUES 27-266
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Description: PLASMID DERIVED NON-GENOMIC / Plasmid: OPINF VECTOR BASED ON PTRIEX VECTOR / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9K2N0, beta-lactamase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / 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: 2.32 Å3/Da / Density % sol: 47 %
Description: TORSION ANGLES OF ASP 84, TRP 87 AND ALA 178 LAY OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS HOWEVER CLEAR ELECTRON DENSITY VALIDATED THE PROPOSED CONFORMATIONS.
Crystal growDetails: 0.2 M MAGNESIUM FORMATE, 20 % W/V PEG3350, 1 MM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9163
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9163 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 101604 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 9.93 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.9
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.5 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KO3

1ko3


Resolution: 1.294→39.844 Å / SU ML: 0.1 / σ(F): 1.34 / Phase error: 11.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1375 2008 2 %
Rwork0.1126 --
obs0.1131 101596 97.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.37 Å2
Refinement stepCycle: LAST / Resolution: 1.294→39.844 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3477 0 23 497 3997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0253832
X-RAY DIFFRACTIONf_angle_d1.2395288
X-RAY DIFFRACTIONf_dihedral_angle_d12.6631351
X-RAY DIFFRACTIONf_chiral_restr0.077587
X-RAY DIFFRACTIONf_plane_restr0.006703
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2942-1.32650.18791360.14946616X-RAY DIFFRACTION91
1.3265-1.36240.14891370.11647114X-RAY DIFFRACTION98
1.3624-1.40250.12181480.0997079X-RAY DIFFRACTION98
1.4025-1.44780.13731510.09647115X-RAY DIFFRACTION98
1.4478-1.49950.15921460.09587077X-RAY DIFFRACTION98
1.4995-1.55960.13031390.08566990X-RAY DIFFRACTION96
1.5596-1.63050.12511430.08397196X-RAY DIFFRACTION99
1.6305-1.71650.1291440.08217219X-RAY DIFFRACTION99
1.7165-1.82410.12051450.0867155X-RAY DIFFRACTION99
1.8241-1.96490.11021480.09237166X-RAY DIFFRACTION99
1.9649-2.16260.11631360.0967068X-RAY DIFFRACTION97
2.1626-2.47550.14711450.1127253X-RAY DIFFRACTION100
2.4755-3.11870.14881480.13177314X-RAY DIFFRACTION100
3.1187-39.86340.1471420.14287226X-RAY DIFFRACTION98

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