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- PDB-2y87: Native VIM-7. Structural and computational investigations of VIM-... -

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Basic information

Entry
Database: PDB / ID: 2y87
TitleNative VIM-7. Structural and computational investigations of VIM-7: Insights into the substrate specificity of VIM metallo-beta- lactamases
ComponentsMETALLO-B-LACTAMASE
KeywordsHYDROLASE / CEPHALOSPORINS / ANTIBIOTIC RECOGNITION
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / : / 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
Metallo-beta-lactamase VIM-7
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsSaradhi, P. / Leiros, H.-K.S. / Ahmad, R. / Spencer, J. / Leiros, I. / Walsh, T.R. / Sundsfjord, A. / Samuelsen, O.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structural and Computational Investigations of Vim- 7: Insights Into the Substrate Specificity of Vim Metallo-Beta-Lactamases
Authors: Saradhi, P. / Leiros, H.-K.S. / Ahmad, R. / Spencer, J. / Leiros, I. / Walsh, T.R. / Sundsfjord, A. / Samuelsen, O.
History
DepositionFeb 3, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2011Group: Database references / 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_alt_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_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_alt_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.pdbx_ptnr2_label_alt_id / _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: METALLO-B-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2975
Polymers28,1421
Non-polymers1554
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.399, 70.399, 47.562
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein METALLO-B-LACTAMASE / METALLO-BETA-LACTAMASE VIM-7 / METALLO-BETA-LACTAMASE


Mass: 28141.846 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q840P9
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsMICROHETEROGENEITY OBSERVED BETWEEN SULPHUR OF UNX A1296 AND HOH A2000. THE AUTHOR SUGGESTS THE ...MICROHETEROGENEITY OBSERVED BETWEEN SULPHUR OF UNX A1296 AND HOH A2000. THE AUTHOR SUGGESTS THE IDENTITY OF THE UNX ION IS SULPHUR
Sequence detailsAUTHOR DEFINED DISCONTINUOUS RESIDUE NUMBERING. THE SEQUENCE IS NUMBERED ACCORDING TO THE BBL ...AUTHOR DEFINED DISCONTINUOUS RESIDUE NUMBERING. THE SEQUENCE IS NUMBERED ACCORDING TO THE BBL NUMBERING SCHEME (REFERENCE GARAU, G. ET AL (2004). UPDATE OF THE STANDARD NUMBERING SCHEME FOR CLASS B B -LACTAMASES. ANTIMICROB. AGENTS CHEMOTHER. 48, 2347-9.) HENCE GIVING INCONSECUTIVE NUMBERING OF RESIDUES.

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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: 1.97 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growpH: 5
Details: 22.5-23.5% POLYETHYLENE GLYCOL MONOMETHYL ETHERS (PEG MME) 2K, 0.1 M CALCIUM ACETATE, 0.1 M SODIUM CACODYLATE PH 5.0, 8 MM BETA-MERCAPTOETHANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.24
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 1.86→29 Å / Num. obs: 19415 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.9
Reflection shellResolution: 1.86→1.96 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4 / % possible all: 82.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KO3

1ko3


Resolution: 1.86→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.606 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21011 1984 10.2 %RANDOM
Rwork0.16023 ---
obs0.16531 17386 97.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.396 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.86→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1705 0 4 170 1879
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221734
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6851.9522356
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7845219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.08823.97373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80415260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3061511
X-RAY DIFFRACTIONr_chiral_restr0.1270.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211293
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_it0.991.51121
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.70221791
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7823613
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.7214.5565
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.855→1.903 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 113 -
Rwork0.3 915 -
obs--70.46 %

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