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- PDB-7w3w: X-ray structure of apo-VmFbpA, a ferric ion-binding protein from ... -

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Basic information

Entry
Database: PDB / ID: 7w3w
TitleX-ray structure of apo-VmFbpA, a ferric ion-binding protein from Vibrio metschnikovii
ComponentsIron-utilization periplasmic protein
KeywordsMETAL BINDING PROTEIN / FbpA / ABC transporter / iron
Function / homology: / Ferric binding protein / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / metal ion binding / Iron-utilization periplasmic protein
Function and homology information
Biological speciesVibrio metschnikovii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.858 Å
AuthorsLu, P. / Sui, M. / Zhang, M. / Nagata, K.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20K22561 Japan
Japan Society for the Promotion of Science (JSPS)18H02151 Japan
Japan Society for the Promotion of Science (JSPS)19H03045 Japan
Japan Society for the Promotion of Science (JSPS)19H05771 Japan
CitationJournal: Int J Mol Sci / Year: 2021
Title: Rosmarinic Acid and Sodium Citrate Have a Synergistic Bacteriostatic Effect against Vibrio Species by Inhibiting Iron Uptake.
Authors: Lu, P. / Sui, M. / Zhang, M. / Wang, M. / Kamiya, T. / Okamoto, K. / Itoh, H. / Okuda, S. / Suzuki, M. / Asakura, T. / Fujiwara, T. / Nagata, K.
History
DepositionNov 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Iron-utilization periplasmic protein


Theoretical massNumber of molelcules
Total (without water)33,5011
Polymers33,5011
Non-polymers00
Water4,017223
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)90.792, 90.792, 149.836
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-594-

HOH

21A-608-

HOH

31A-623-

HOH

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Components

#1: Protein Iron-utilization periplasmic protein


Mass: 33500.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio metschnikovii (bacteria) / Gene: fbpA, NCTC8563_00091 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A380N8Q9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.66 Å3/Da / Density % sol: 53.77 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 7
Details: 0.25M ammonium tartrate dibasic, 25% PEG 3350, 100mM Tris-HCl (pH 7.0)

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
1277.151N
2277.151N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL44XU10.899995
SYNCHROTRONPhoton Factory AR-NE3A21
Detector
TypeIDDetectorDate
DECTRIS EIGER X 16M1PIXELNov 13, 2020
DECTRIS PILATUS 2M-F2PIXELDec 21, 2020
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.8999951
211
ReflectionResolution: 1.858→45.437 Å / Num. obs: 58147 / % possible obs: 99.8 % / Redundancy: 7.85 % / CC1/2: 0.999 / Net I/σ(I): 15.17
Reflection shellResolution: 1.86→1.97 Å / Num. unique obs: 25021 / CC1/2: 0.999

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WAE

3wae


Resolution: 1.858→45.437 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / SU ML: 0 / Cross valid method: FREE R-VALUE / ESU R: 0.103 / ESU R Free: 0.116
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2079 1499 4.77 %
Rwork0.185 29929 -
all0.186 --
obs-31428 99.759 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.803 Å2
Baniso -1Baniso -2Baniso -3
1-0.018 Å20.009 Å20 Å2
2--0.018 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.858→45.437 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2364 0 0 223 2587
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.858-1.9060.2261080.2222110X-RAY DIFFRACTION97.8817
1.906-1.9580.2321150.1972104X-RAY DIFFRACTION99.955
1.958-2.0150.2531010.1932077X-RAY DIFFRACTION100
2.015-2.0770.198970.1821990X-RAY DIFFRACTION100
2.077-2.1450.222970.1771953X-RAY DIFFRACTION100
2.145-2.220.208920.1751886X-RAY DIFFRACTION99.9495
2.22-2.3040.1841120.1791793X-RAY DIFFRACTION100
2.304-2.3980.18800.1791774X-RAY DIFFRACTION100
2.398-2.5050.235860.1861690X-RAY DIFFRACTION100
2.505-2.6270.222890.1861596X-RAY DIFFRACTION99.9407
2.627-2.7690.203660.1821560X-RAY DIFFRACTION100
2.769-2.9360.206720.1851474X-RAY DIFFRACTION99.9354
2.936-3.1390.198710.1851391X-RAY DIFFRACTION100
3.139-3.390.186620.1841285X-RAY DIFFRACTION99.9258
3.39-3.7130.207560.1741209X-RAY DIFFRACTION100
3.713-4.150.185430.1711119X-RAY DIFFRACTION99.914
4.15-4.790.194470.172981X-RAY DIFFRACTION99.709
4.79-5.8610.246410.198847X-RAY DIFFRACTION99.5516
5.861-8.2650.257420.222674X-RAY DIFFRACTION99.5828

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