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- PDB-8j4h: X-ray structure of a ferric ion-binding protein A (FbpA) from Vib... -

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Basic information

Entry
Database: PDB / ID: 8j4h
TitleX-ray structure of a ferric ion-binding protein A (FbpA) from Vibrio metschnikovii in complex with Danshensu (DSS)
ComponentsFerric iron ABC transporter iron-binding protein
KeywordsMETAL BINDING PROTEIN / Ferric Binding Protein / FbpA / Danshensu / Vibrio metschnikovii
Function / homologyFerric binding protein / iron ion transmembrane transport / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / metal ion binding / Chem-TO9 / Ferric iron ABC transporter iron-binding protein
Function and homology information
Biological speciesVibrio metschnikovii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsLu, P. / Jiang, J. / Nagata, K.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20K22561 Japan
The Japan Science Society2023-4016 Japan
Japan Science and TechnologyJPMJSP2108 Japan
Japan Society for the Promotion of Science (JSPS)18H02151 Japan
CitationJournal: Protein Sci. / Year: 2024
Title: Molecular mechanism of Fe 3+ binding inhibition to Vibrio metschnikovii ferric ion-binding protein, FbpA, by rosmarinic acid and its hydrolysate, danshensu.
Authors: Lu, P. / Jiang, J. / Liu, C. / Okuda, S. / Itoh, H. / Okamoto, K. / Suzuki, M. / Nagata, K.
History
DepositionApr 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferric iron ABC transporter iron-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6992
Polymers33,5011
Non-polymers1981
Water4,161231
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12880 Å2
Unit cell
Length a, b, c (Å)90.233, 90.233, 149.475
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-674-

HOH

21A-691-

HOH

31A-711-

HOH

41A-730-

HOH

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Components

#1: Protein Ferric iron ABC transporter iron-binding protein


Mass: 33500.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio metschnikovii (bacteria) / Gene: VIB_000280 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C9P1D3
#2: Chemical ChemComp-TO9 / (2~{R})-3-[3,4-bis(oxidanyl)phenyl]-2-oxidanyl-propanoic acid / Danshensu


Mass: 198.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.62 Å3/Da / Density % sol: 53.09 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 1 M (NH4)2HPO4, 0.1 M imidazole-HCl (pH 8.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.008→49.825 Å / Num. obs: 45218 / % possible obs: 99.3 % / Redundancy: 10.59 % / CC1/2: 0.999 / Net I/σ(I): 15.81
Reflection shellResolution: 2.008→2.018 Å / Num. unique obs: 7187 / CC1/2: 0.713

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata scaling
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→45.12 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.943 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2089 1197 4.9 %RANDOM
Rwork0.15896 ---
obs0.16142 23359 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.308 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.01→45.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2364 0 14 231 2609
LS refinement shellResolution: 2.01→2.06 Å
RfactorNum. reflection% reflection
Rfree0.301 78 -
Rwork0.21 1643 -
obs--96.96 %

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