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- PDB-2wrs: Crystal Structure of the Mono-Zinc Metallo-beta-lactamase VIM-4 f... -

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Basic information

Entry
Database: PDB / ID: 2wrs
TitleCrystal Structure of the Mono-Zinc Metallo-beta-lactamase VIM-4 from Pseudomonas aeruginosa
ComponentsBETA-LACTAMASE VIM-4
KeywordsHYDROLASE
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
CITRIC ACID / CITRATE ANION / beta-lactamase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsLassaux, P. / Hamel, M. / Gulea, M. / Delbruck, H. / Traore, D.A.K. / Mercuri, P.S. / Horsfall, L. / Dehareng, D. / Gaumont, A.-C. / Frere, J.-M. ...Lassaux, P. / Hamel, M. / Gulea, M. / Delbruck, H. / Traore, D.A.K. / Mercuri, P.S. / Horsfall, L. / Dehareng, D. / Gaumont, A.-C. / Frere, J.-M. / Ferrer, J.-L. / Hoffmann, K. / Galleni, M. / Bebrone, C.
CitationJournal: J.Med.Chem. / Year: 2010
Title: Mercaptophosphonate Compounds as Broad-Spectrum Inhibitors of the Metallo-Beta-Lactamases.
Authors: Lassaux, P. / Hamel, M. / Gulea, M. / Delbruck, H. / Mercuri, P.S. / Horsfall, L. / Dehareng, D. / Kupper, M. / Frere, J.-M. / Hoffmann, K. / Galleni, M. / Bebrone, C.
History
DepositionSep 2, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references / Structure summary / Version format compliance
Revision 1.2Dec 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.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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,7868
Polymers48,8922
Non-polymers8936
Water48627
1
A: BETA-LACTAMASE VIM-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0855
Polymers24,4461
Non-polymers6394
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BETA-LACTAMASE VIM-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7013
Polymers24,4461
Non-polymers2552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)140.130, 45.670, 105.030
Angle α, β, γ (deg.)90.00, 105.41, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein BETA-LACTAMASE VIM-4 / METALLO-BETA-LACTAMASE / METALLO-BETA-LACTAMASE VIM-4 / VIM-4 / 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) / Plasmid: PET9A-VIM-4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21-CODONPLUS (DE3) / References: UniProt: Q70E11, beta-lactamase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / 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: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.2 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growpH: 7
Details: 1.55 M AMMONIUM CITRATE TRIBASIC PH 7.0 POWDER OF COMPOUND 18 IN THE DROP.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 16118 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 42.096 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.03
Reflection shellResolution: 2.79→2.96 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.43 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WHG

2whg


Resolution: 2.79→43.27 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.884 / SU B: 29.864 / SU ML: 0.267 / Cross valid method: THROUGHOUT / ESU R Free: 0.346 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25318 806 5 %RANDOM
Rwork0.19861 ---
obs0.20134 15312 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: 38.177 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å20.13 Å2
2---0.35 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.79→43.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3454 0 54 27 3535
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0213594
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210
X-RAY DIFFRACTIONr_angle_refined_deg1.7941.9644923
X-RAY DIFFRACTIONr_angle_other_deg0.984322
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4125460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.33824.14157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.27715513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3731521
X-RAY DIFFRACTIONr_chiral_restr0.1140.2557
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212813
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1621.52292
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.0923687
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.48631302
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1154.51236
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.62933604
X-RAY DIFFRACTIONr_sphericity_free6.572329
X-RAY DIFFRACTIONr_sphericity_bonded2.36133527
LS refinement shellResolution: 2.792→2.864 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 54 -
Rwork0.27 1037 -
obs--100 %

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