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- PDB-1ko3: VIM-2, a Zn-beta-lactamase from Pseudomonas aeruginosa with Cys22... -

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Basic information

Entry
Database: PDB / ID: 1ko3
TitleVIM-2, a Zn-beta-lactamase from Pseudomonas aeruginosa with Cys221 reduced
ComponentsVIM-2 metallo-beta-lactamase
KeywordsHYDROLASE / alpha-beta/beta-alpha fold
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding
Similarity search - Function
: / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / HYDROXIDE ION / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.91 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 / 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_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_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_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: VIM-2 metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8898
Polymers24,5221
Non-polymers3677
Water2,450136
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.805, 78.040, 79.648
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 1 molecules A

#1: Protein VIM-2 metallo-beta-lactamase


Mass: 24522.246 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

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Non-polymers , 5 types, 143 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / 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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HO
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.15 Å3/Da / Density % sol: 42.72 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG8K, 0.1M NaCac/Cac.acid, 0.2M Na acetate, 0.5mM TCEP, 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: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 24, 2001 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.91→51.63 Å / Num. all: 16087 / Num. obs: 15030 / % possible obs: 90.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.052 / Rsym value: 0.045 / Net I/σ(I): 12.6
Reflection shellResolution: 1.91→2.02 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.171 / Mean I/σ(I) obs: 5.4 / Num. unique all: 544 / Rsym value: 0.135 / % possible all: 50
Reflection
*PLUS
Highest resolution: 1.9 Å / % possible obs: 91 % / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 50 % / Rmerge(I) obs: 0.14

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
CNS1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: VIM-2 oxidized, PDB ID code 1KO2

1ko2


Resolution: 1.91→25 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2504 1439 9.76 %random
Rwork0.2091 ---
all-16633 --
obs-14741 88.6 %-
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.91→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1733 0 13 136 1882
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_improper_angle_d0.95
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDRfactor Rfree errorNum. reflection obs
1.91-2.030.3171490.254X-RAY DIFFRACTION0.0261214
2.31-2.360.2529510.2203X-RAY DIFFRACTION520
4.61-5.810.2597650.1895X-RAY DIFFRACTION532
Refinement
*PLUS
Highest resolution: 1.9 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.95
LS refinement shell
*PLUS
Lowest resolution: 2.02 Å

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