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- PDB-8j4j: X-ray structure of a ferric ion-binding protein A (FbpA) from Vib... -

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Basic information

Entry
Database: PDB / ID: 8j4j
TitleX-ray structure of a ferric ion-binding protein A (FbpA) from Vibrio metschnikovii in complex with ferric ion
ComponentsFerric iron ABC transporter iron-binding protein
KeywordsMETAL BINDING PROTEIN / Ferric Binding Protein / FbpA / Danshensu / Vibrio metschnikovii
Function / homologyiron ion transmembrane transport / Ferric binding protein / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / metal ion binding / CARBONATE ION / : / Ferric iron ABC transporter iron-binding protein
Function and homology information
Biological speciesVibrio metschnikovii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsLu, P. / Jiang, J. / Nagata, K.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20K22561 Japan
Other privateThe Japan Science Society 2023-4016 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)33,6774
Polymers33,5011
Non-polymers1763
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.522, 91.522, 150.454
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-541-

HOH

21A-618-

HOH

31A-619-

HOH

41A-625-

HOH

51A-627-

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-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.72 Å3/Da / Density % sol: 54.72 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M magnesium formate dihydrate, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.899995 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.899995 Å / Relative weight: 1
ReflectionResolution: 2.15→43.82 Å / Num. obs: 38034 / % possible obs: 99.5 % / Redundancy: 10.26 % / CC1/2: 0.999 / Net I/σ(I): 11.02
Reflection shellResolution: 2.15→2.16 Å / Mean I/σ(I) obs: 1.19 / Num. unique obs: 1457 / CC1/2: 0.789

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→43.78 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.958 / SU B: 17.198 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24188 1052 5.1 %RANDOM
Rwork0.16944 ---
obs0.17301 19724 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.127 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0.08 Å2-0 Å2
2---0.15 Å20 Å2
3---0.49 Å2
Refinement stepCycle: 1 / Resolution: 2.15→43.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2364 0 9 128 2501
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122416
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162309
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.6493283
X-RAY DIFFRACTIONr_angle_other_deg0.4781.5655303
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9575308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.054511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.03910393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0610.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022887
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02551
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.1066.2921235
X-RAY DIFFRACTIONr_mcbond_other5.1076.2921235
X-RAY DIFFRACTIONr_mcangle_it6.44311.3021542
X-RAY DIFFRACTIONr_mcangle_other6.44211.3041543
X-RAY DIFFRACTIONr_scbond_it6.9376.961181
X-RAY DIFFRACTIONr_scbond_other6.9176.9431176
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.77112.4281736
X-RAY DIFFRACTIONr_long_range_B_refined12.15960.812808
X-RAY DIFFRACTIONr_long_range_B_other12.02960.592789
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.153→2.209 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.459 75 -
Rwork0.427 1346 -
obs--94.29 %
Refinement TLS params.Method: refined / Origin x: -22.8891 Å / Origin y: -36.8705 Å / Origin z: -18.5805 Å
111213212223313233
T0.0375 Å20.0207 Å20.0002 Å2-0.0684 Å20.0041 Å2--0.0068 Å2
L0.3863 °2-0.2065 °2-0.0071 °2-0.8617 °20.0851 °2--0.1835 °2
S-0.0153 Å °-0.021 Å °-0.0288 Å °-0.0448 Å °0.0257 Å °0.0641 Å °-0.0387 Å °-0.0199 Å °-0.0104 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 100
2X-RAY DIFFRACTION1A101 - 309

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