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- PDB-2whg: Crystal Structure of the Di-Zinc Metallo-beta-lactamase VIM-4 fro... -

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Basic information

Entry
Database: PDB / ID: 2whg
TitleCrystal Structure of the Di-Zinc Metallo-beta-lactamase VIM-4 from Pseudomonas aeruginosa
ComponentsVIM-4 METALLO-BETA-LACTAMASE
KeywordsHYDROLASE / ALPHA-BETA/BETA-ALPHA FOLD
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / periplasmic space / hydrolase activity / response to antibiotic / 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
CITRATE ANION / beta-lactamase / beta-lactamase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLassaux, P. / Traore, D.A.K. / Galleni, M. / Ferrer, J.L.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2011
Title: Biochemical and Structural Characterization of the Subclass B1 Metallo-{Beta}-Lactamase Vim-4.
Authors: Lassaux, P. / Traore, D.A.K. / Loisel, E. / Favier, A. / Docquier, J.D. / Sohier, J.S. / Laurent, C. / Bebrone, C. / Frere, J.M. / Ferrer, J.L. / Galleni, M.
History
DepositionMay 5, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2011Group: Database references / Version format compliance
Revision 1.2Dec 13, 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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.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_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

Downloads & links

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Assembly

Deposited unit
A: VIM-4 METALLO-BETA-LACTAMASE
B: VIM-4 METALLO-BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5328
Polymers48,8922
Non-polymers6406
Water7,837435
1
A: VIM-4 METALLO-BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7664
Polymers24,4461
Non-polymers3203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: VIM-4 METALLO-BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7664
Polymers24,4461
Non-polymers3203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)141.390, 46.220, 105.990
Angle α, β, γ (deg.)90.00, 105.24, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein VIM-4 METALLO-BETA-LACTAMASE


Mass: 24446.150 Da / Num. of mol.: 2 / Fragment: RESIDUES 32-261
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Description: GENE BLAVIM-4 / Plasmid: PET9A-VIM-4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21-CODONPLUS (DE3)
References: UniProt: Q70E11, UniProt: Q8KRJ3*PLUS, beta-lactamase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / 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: 3.3 Å3/Da / Density % sol: 63 % / Description: NONE
Crystal growpH: 7 / Details: 1.55 M AMMONIUM CITRATE TRIBASIC PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.9→47.3 Å / Num. obs: 52283 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 26.59 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.92
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.59 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KO3

1ko3


Resolution: 1.9→47.3 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.909 / SU B: 8.864 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2615 5 %RANDOM
Rwork0.2 ---
obs0.202 49667 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.52 Å2
Baniso -1Baniso -2Baniso -3
1-1.67 Å20 Å2-0.4 Å2
2---1.02 Å20 Å2
3----0.86 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3454 0 30 435 3919
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0213613
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4241.9564952
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3375468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.77224.037161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.41115522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6791523
X-RAY DIFFRACTIONr_chiral_restr0.0990.2561
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022839
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1920.21577
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22406
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2366
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0780.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.218
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2310.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0231.52362
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.57923731
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.27831398
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3624.51221
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.4833760
X-RAY DIFFRACTIONr_sphericity_free7.2593440
X-RAY DIFFRACTIONr_sphericity_bonded3.97533530
LS refinement shellResolution: 1.9→1.94 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 180 -
Rwork0.33 3408 -
obs--100 %

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