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- PDB-1ko2: VIM-2, a Zn-beta-lactamase from Pseudomonas aeruginosa with an ox... -

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Basic information

Entry
Database: PDB / ID: 1ko2
TitleVIM-2, a Zn-beta-lactamase from Pseudomonas aeruginosa with an oxidized Cys (cysteinesulfonic)
ComponentsVIM-2 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
ACETATE ION / beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGarcia-Saez, I. / Docquier, J.-D. / Rossolini, G.M. / Dideberg, O.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: The three-dimensional structure of VIM-2, a Zn-beta-lactamase from Pseudomonas aeruginosa in its reduced and oxidised form
Authors: Garcia-Saez, I. / Docquier, J.-D. / Rossolini, G.M. / Dideberg, O.
History
DepositionDec 20, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 2, 2003Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VIM-2 metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8195
Polymers24,5701
Non-polymers2494
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.180, 78.030, 80.130
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 VIM-2 metallo-beta-lactamase


Mass: 24570.244 Da / Num. of mol.: 1 / Fragment: residues 30-295
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaVIM-2 / Plasmid: PET9-VIM-2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9K2N0, 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS COORDINATES IS USED NON-SEQUENTIAL RESIDUE NUMBERING. MANY NUMBERS WERE SIMPLY SKIPPED IN THE ...THIS COORDINATES IS USED NON-SEQUENTIAL RESIDUE NUMBERING. MANY NUMBERS WERE SIMPLY SKIPPED IN THE NUMBERING AND HAVE NOTHING TO DO WITH LACK OF ELECTRON DENSITY. RESIDUES IN THE STRUCTURE ARE NUMBERED FOLLOWING THE STANDARD NUMBERING FOR CLASS B BETA-LACTAMASES (BBL NUMBERING) (GALLENI, M. ET AL. (2001). "STANDARD NUMBERING SCHEME FOR CLASS B BETA-LACTAMASES". ANTIMICROB. AGENTS CHEMOTHER. MARCH, P. 660-663).

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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: 2.02 Å3/Da / Density % sol: 38.49 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG8K, 0.2M Na acetate, 0.1M NaCac./Cac.acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15.5 mg/mlprotein1drop
210 mMHEPES1droppH7.5
30.2 M1dropNaCl
41 mMdithiothreitol1drop
530 %PEG80001reservoir
60.2 Msodium acetate1reservoir
70.1 Msodium cacodylate1reservoirpH6.5
810000 nM1reservoirZnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.78→30 Å / Num. all: 34075 / Num. obs: 20045 / % possible obs: 69 % / Observed criterion σ(I): 3 / Redundancy: 13 % / Biso Wilson estimate: 16.4 Å2
Reflection shellResolution: 1.78→1.85 Å / % possible all: 49.2
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. obs: 10623 / % possible obs: 96 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.32 Å / % possible obs: 87.8 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 4.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB-ENTRY 1BVT

1bvt


Resolution: 2.2→21.45 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2475054.4 / Data cutoff low absF: 0 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2506 994 9.8 %random
Rwork0.2088 ---
all-19877 --
obs-10190 94 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.0734 Å2 / ksol: 0.367294 e/Å3
Displacement parametersBiso mean: 22.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.21 Å20 Å20 Å2
2--2.64 Å20 Å2
3----4.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.2→21.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1736 0 10 115 1861
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d1.5
X-RAY DIFFRACTIONc_mcbond_it0.581.5
X-RAY DIFFRACTIONc_mcangle_it1.042
X-RAY DIFFRACTIONc_scbond_it0.62
X-RAY DIFFRACTIONc_scangle_it0.962.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.349 148 10 %
Rwork0.251 1338 -
obs--83.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramacet.top
X-RAY DIFFRACTION3water.param
X-RAY DIFFRACTION4acet.param
Refinement
*PLUS
Highest resolution: 2.2 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.251 / Rfactor Rwork: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.5
LS refinement shell
*PLUS
Lowest resolution: 2.32 Å

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