[English] 日本語
Yorodumi
- PDB-8j4j: X-ray structure of a ferric ion-binding protein A (FbpA) from Vib... -

+
Open data


ID or keywords:

Loading...

-
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 / homologyFerric binding protein / iron ion transmembrane transport / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more