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- PDB-4uws: VIM-26-PEG. Leu224 in VIM-26 from Klebsiella pneumoniae has impli... -

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Basic information

Entry
Database: PDB / ID: 4uws
TitleVIM-26-PEG. Leu224 in VIM-26 from Klebsiella pneumoniae has implications for drug binding.
ComponentsMETALLO-BETA-LACTAMASE VIM-26
KeywordsHYDROLASE / ANTIBIOTIC RESISTANCE / DRUG BINDING SITE
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / 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
DI(HYDROXYETHYL)ETHER / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKLEBSIELLA PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsLeiros, H.-K.S. / Edvardsen, K.S.W. / Bjerga, G.E.K. / Samuelsen, O.
CitationJournal: FEBS J. / Year: 2015
Title: Structural and Biochemical Characterization of Vim-26 Show that Leu224 Has Implications for the Substrate Specificity of Vim Metallo-Beta-Lactamases.
Authors: Leiros, H.S. / Edvardsen, K.S.W. / Bjerga, G.E.K. / Samuelsen, O.
History
DepositionAug 14, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
Revision 2.0Oct 23, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other
Category: atom_site / pdbx_database_status ...atom_site / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Jan 10, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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.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

Downloads & links

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Assembly

Deposited unit
B: METALLO-BETA-LACTAMASE VIM-26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4696
Polymers28,0741
Non-polymers3955
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.759, 68.172, 40.406
Angle α, β, γ (deg.)90.00, 92.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules B

#1: Protein METALLO-BETA-LACTAMASE VIM-26


Mass: 28074.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) KLEBSIELLA PNEUMONIAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E5BDC6

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Non-polymers , 5 types, 163 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details1,2-ETHANEDIOL (EDO): ALSO CALLED ETHYLENE GLYCOL

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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: 2.09 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growpH: 9.5
Details: 21% POLYETHYLENE GLYCOL MONOMETHYL ETHERS (PEG MME) 5K, 0.1 M CHES BUFFER AT PH 9.5, 0.1 M MAGNESIUM FORMATE AND 4% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.66→40 Å / Num. obs: 24661 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 19.77 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.6
Reflection shellResolution: 1.66→1.75 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.3 / % possible all: 81.1

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Processing

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

2y8b


Resolution: 1.66→22.072 Å / SU ML: 0.15 / σ(F): 1.35 / Phase error: 20.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2 1245 5.1 %
Rwork0.1561 --
obs0.1583 24629 96.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.66→22.072 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1722 0 18 158 1898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131853
X-RAY DIFFRACTIONf_angle_d1.3012549
X-RAY DIFFRACTIONf_dihedral_angle_d14.801650
X-RAY DIFFRACTIONf_chiral_restr0.077286
X-RAY DIFFRACTIONf_plane_restr0.006336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.72650.29721180.23422076X-RAY DIFFRACTION78
1.7265-1.8050.27751240.20792472X-RAY DIFFRACTION92
1.805-1.90010.24411490.17752653X-RAY DIFFRACTION100
1.9001-2.01910.19871570.15722668X-RAY DIFFRACTION100
2.0191-2.17490.19911250.13662675X-RAY DIFFRACTION100
2.1749-2.39350.1921430.14522708X-RAY DIFFRACTION100
2.3935-2.73930.17281350.1412691X-RAY DIFFRACTION100
2.7393-3.44910.18461450.14532708X-RAY DIFFRACTION100
3.4491-22.07410.1991490.16162733X-RAY DIFFRACTION100

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