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- PDB-4d1t: High resolution structure of native tVIM-7 from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 4d1t
TitleHigh resolution structure of native tVIM-7 from Pseudomonas aeruginosa
ComponentsMETALLO-B-LACTAMASE
KeywordsHYDROLASE / RESIDUE DETERMINANTS / LIGAND INTERACTION
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: 1.25 Å
AuthorsLeiros, H.-K.S. / Skagseth, S. / Edvardsen, K.S.W. / Lorentzen, M.S. / Bjerga, G.E.K. / Leiros, I. / Samuelsen, O.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2014
Title: His224 Alters the R2 Drug Binding Site and Phe218 Influences the Catalytic Efficiency in the Metallo-Beta-Lactamase Vim-7.
Authors: Leiros, H.-K.S. / Skagseth, S. / Edvardsen, K.S.W. / Lorentzen, M.S. / Bjerga, G.E.K. / Leiros, I. / Samuelsen, O.
History
DepositionMay 5, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Atomic model
Revision 1.2Aug 13, 2014Group: Database references
Revision 1.3Dec 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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: METALLO-B-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2643
Polymers28,1331
Non-polymers1312
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.979, 69.979, 47.530
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


Mass: 28132.877 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) / Variant (production host): STAR / References: UniProt: Q840P9
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.07 Å3/Da / Density % sol: 40.53 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.25→30 Å / Num. obs: 61189 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 9.2 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.1
Reflection shellResolution: 1.23→1.32 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2 / % possible all: 78.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y8B

2y8b


Resolution: 1.25→23.326 Å / SU ML: 0.1 / σ(F): 1.34 / Phase error: 13.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1483 2472 4 %
Rwork0.1307 --
obs0.1315 61161 96.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.5 Å2
Refinement stepCycle: LAST / Resolution: 1.25→23.326 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1718 0 2 280 2000
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111896
X-RAY DIFFRACTIONf_angle_d1.3862608
X-RAY DIFFRACTIONf_dihedral_angle_d13.775686
X-RAY DIFFRACTIONf_chiral_restr0.078296
X-RAY DIFFRACTIONf_plane_restr0.007346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2503-1.27440.2639950.23442244X-RAY DIFFRACTION67
1.2744-1.30040.2466950.21382708X-RAY DIFFRACTION80
1.3004-1.32870.23081290.18453029X-RAY DIFFRACTION90
1.3287-1.35960.19561370.16943282X-RAY DIFFRACTION96
1.3596-1.39360.1941370.14283369X-RAY DIFFRACTION100
1.3936-1.43120.15661590.12543341X-RAY DIFFRACTION100
1.4312-1.47330.14631340.12163356X-RAY DIFFRACTION100
1.4733-1.52090.15181430.10643372X-RAY DIFFRACTION100
1.5209-1.57520.13781400.09963391X-RAY DIFFRACTION100
1.5752-1.63830.14531410.09853389X-RAY DIFFRACTION100
1.6383-1.71280.10781370.09783358X-RAY DIFFRACTION100
1.7128-1.80310.11421420.0983413X-RAY DIFFRACTION100
1.8031-1.9160.13421330.10413362X-RAY DIFFRACTION100
1.916-2.06390.11161560.11113420X-RAY DIFFRACTION100
2.0639-2.27140.13041440.11483384X-RAY DIFFRACTION100
2.2714-2.59970.13871520.12753402X-RAY DIFFRACTION100
2.5997-3.27390.15721450.14533421X-RAY DIFFRACTION100
3.2739-23.33040.15871530.15263448X-RAY DIFFRACTION99

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