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- PDB-4d1u: A D120A mutant of VIM-7 from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 4d1u
TitleA D120A mutant of VIM-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; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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_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
A: METALLO-B-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1632
Polymers28,0981
Non-polymers651
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.764, 69.764, 47.286
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: 28097.834 Da / Num. of mol.: 1 / Mutation: YES
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.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.04 Å3/Da / Density % sol: 39.84 % / 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: 1.8→40 Å / Num. obs: 21271 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 18.36 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

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

2y8b


Resolution: 1.8→24.665 Å / SU ML: 0.2 / σ(F): 1.4 / Phase error: 18.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2075 1091 5.1 %
Rwork0.1606 --
obs0.163 21244 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.3 Å2
Refinement stepCycle: LAST / Resolution: 1.8→24.665 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1695 0 1 152 1848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121767
X-RAY DIFFRACTIONf_angle_d1.2982423
X-RAY DIFFRACTIONf_dihedral_angle_d13.582625
X-RAY DIFFRACTIONf_chiral_restr0.086282
X-RAY DIFFRACTIONf_plane_restr0.006317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8003-1.88220.28421450.21892507X-RAY DIFFRACTION100
1.8822-1.98140.21421310.18652486X-RAY DIFFRACTION100
1.9814-2.10540.22131470.16352512X-RAY DIFFRACTION100
2.1054-2.26790.19241250.15352504X-RAY DIFFRACTION100
2.2679-2.49590.19241450.15562500X-RAY DIFFRACTION100
2.4959-2.85660.24051380.1622507X-RAY DIFFRACTION100
2.8566-3.59730.20151480.15952520X-RAY DIFFRACTION100
3.5973-24.66760.18351120.14842617X-RAY DIFFRACTION100

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