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- PDB-4uwr: Mono-zinc VIM-26. Leu224 in VIM-26 from Klebsiella pneumoniae has... -

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Basic information

Entry
Database: PDB / ID: 4uwr
TitleMono-zinc VIM-26. 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 / periplasmic space / 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
FORMIC ACID / beta-lactamase
Similarity search - Component
Biological speciesKLEBSIELLA PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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 1.2Jan 10, 2024Group: 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_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.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.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)28,2325
Polymers28,0741
Non-polymers1574
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.735, 67.783, 40.408
Angle α, β, γ (deg.)90.00, 93.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.09 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: 1.55→40 Å / Num. obs: 30941 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 18.69 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.3
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.4 / % possible all: 96.3

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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: 1.55→22.07 Å / SU ML: 0.16 / σ(F): 1.35 / Phase error: 19.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1822 1560 5.1 %
Rwork0.1538 --
obs0.1553 30899 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→22.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1718 0 6 163 1887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011817
X-RAY DIFFRACTIONf_angle_d1.2422497
X-RAY DIFFRACTIONf_dihedral_angle_d13.486639
X-RAY DIFFRACTIONf_chiral_restr0.049286
X-RAY DIFFRACTIONf_plane_restr0.006332
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.60.29211300.27152526X-RAY DIFFRACTION94
1.6-1.65720.25341360.22742655X-RAY DIFFRACTION99
1.6572-1.72350.22371480.19742671X-RAY DIFFRACTION100
1.7235-1.80190.21331460.1782650X-RAY DIFFRACTION100
1.8019-1.89690.19891510.16522683X-RAY DIFFRACTION100
1.8969-2.01570.1851410.15362675X-RAY DIFFRACTION100
2.0157-2.17120.17341320.14152672X-RAY DIFFRACTION100
2.1712-2.38940.19221430.1442684X-RAY DIFFRACTION100
2.3894-2.73460.20111320.13942701X-RAY DIFFRACTION100
2.7346-3.44320.161500.1412696X-RAY DIFFRACTION100
3.4432-22.07210.16061510.14812726X-RAY DIFFRACTION100

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