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- PDB-7afy: Crystal structure of the metallo-beta-lactamase VIM1 with 1306 -

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Basic information

Entry
Database: PDB / ID: 7afy
TitleCrystal structure of the metallo-beta-lactamase VIM1 with 1306
ComponentsBeta-lactamase VIM-1
KeywordsHYDROLASE / HYDROLASES / MBL / ANTIBIOTIC RESISTANCE
Function / homology
Function and homology information


beta-lactamase / metal ion binding
Similarity search - Function
: / : / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
Chem-RBW / beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.105 Å
AuthorsBrem, J. / Schofield, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Innovative Medicines InitiativeEnable United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of the metallo-beta-lactamase VIM2 with 139
Authors: Brem, J. / Schofield, C.J.
History
DepositionSep 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase VIM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0176
Polymers25,4341
Non-polymers5835
Water5,531307
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint-103 kcal/mol
Surface area9460 Å2
Unit cell
Length a, b, c (Å)39.648, 68.015, 40.236
Angle α, β, γ (deg.)90.000, 92.940, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase VIM-1 / Class B carbapenemase VIM-1 / Metallo-beta-lactamase / Metallo-beta-lactamase VIM-1 / Metallobeta- ...Class B carbapenemase VIM-1 / Metallo-beta-lactamase / Metallo-beta-lactamase VIM-1 / Metallobeta-lactamase / Subclass B1 metallo-beta-lactamase VIM-1 / VIM-1 / VIM-1 metallo-beta-lactamase / VIM-1 protein


Mass: 25434.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: blaVIM, blaVIM-1, CAZ10_38240, CAZ10_38245, F7O93_29240, F7O93_29270
Production host: Escherichia coli (E. coli) / References: UniProt: Q9XAY4
#2: Chemical ChemComp-RBW / 3-[3-chloranyl-4-(methylsulfonylmethyl)phenyl]-7-propan-2-yl-1~{H}-indole-2-carboxylic acid


Mass: 405.895 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20ClNO4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.13 Å3/Da / Density % sol: 42.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 2.2M ammonium phosphate 0.1M TrisHCl, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97956 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97956 Å / Relative weight: 1
ReflectionResolution: 1.1→40.183 Å / Num. obs: 83848 / % possible obs: 98.5 % / Redundancy: 6.1 % / Biso Wilson estimate: 9.66 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.037 / Rrim(I) all: 0.094 / Net I/σ(I): 13.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.11-1.164.60.49453657115700.8540.2550.5592.993.4
3.49-40.186.50.0631795727660.9940.0270.06828.599.7

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N5I

5n5i


Resolution: 1.105→40.183 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 14.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1452 4169 4.98 %
Rwork0.126 79568 -
obs0.127 83737 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 47.83 Å2 / Biso mean: 16.2205 Å2 / Biso min: 6.55 Å2
Refinement stepCycle: final / Resolution: 1.105→40.183 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1729 0 96 324 2149
Biso mean--13.82 28.82 -
Num. residues----233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091981
X-RAY DIFFRACTIONf_angle_d1.1262743
X-RAY DIFFRACTIONf_chiral_restr0.094299
X-RAY DIFFRACTIONf_plane_restr0.008367
X-RAY DIFFRACTIONf_dihedral_angle_d14.605706
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.1052-1.11780.27731140.2424224283
1.1178-1.13090.2331300.2236249093
1.1309-1.14470.22221460.2153259897
1.1447-1.15920.22581560.2007257898
1.1592-1.17450.20161460.1868268899
1.1745-1.19050.1721270.1782263299
1.1905-1.20760.19741390.1722266699
1.2076-1.22560.17771270.1647266399
1.2256-1.24470.18061110.1579268499
1.2447-1.26510.19141320.1585265899
1.2651-1.2870.18791390.1516265299
1.287-1.31040.161430.1501265299
1.3104-1.33560.15771260.1344267999
1.3356-1.36280.15391290.11942695100
1.3628-1.39250.14291750.1122613100
1.3925-1.42490.14341640.1155266999
1.4249-1.46050.14871680.10422650100
1.4605-1.50.13691580.09952647100
1.5-1.54410.11491420.0991269399
1.5441-1.5940.12231490.0986266199
1.594-1.65090.12311370.0983270199
1.6509-1.7170.12451300.1015269699
1.717-1.79520.11891460.09942669100
1.7952-1.88980.14361480.10612691100
1.8898-2.00820.13921310.10552689100
2.0082-2.16330.12551040.1132713100
2.1633-2.3810.12021090.11922749100
2.381-2.72540.14531470.1256269799
2.7254-3.43350.14941660.12652691100
3.4335-40.10.13721300.132762100

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