[English] 日本語
Yorodumi
- PDB-3a1t: Crystal structue of the cytosolic domain of T. maritima FeoB iron... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3a1t
TitleCrystal structue of the cytosolic domain of T. maritima FeoB iron iransporter in GDP form II
ComponentsIron(II) transport protein B
KeywordsTRANSPORT PROTEIN / FeoB / iron transpoter / small GTPase / G protein / GDI
Function / homology
Function and homology information


ferrous iron transmembrane transporter activity / GTP binding / metal ion binding / plasma membrane
Similarity search - Function
Helix Hairpins - #1770 / FeoB, cytosolic helical domain / FeoB cytosolic helical domain / Ferrous iron transport protein B, C-terminal / Ferrous iron transport protein B C terminus / Ferrous iron transport protein B / FeoB-type guanine nucleotide-binding (G) domain / Ferrous iron transport protein B / FeoB-type guanine nucleotide-binding (G) domain profile. / Nucleoside transporter/FeoB GTPase, Gate domain ...Helix Hairpins - #1770 / FeoB, cytosolic helical domain / FeoB cytosolic helical domain / Ferrous iron transport protein B, C-terminal / Ferrous iron transport protein B C terminus / Ferrous iron transport protein B / FeoB-type guanine nucleotide-binding (G) domain / Ferrous iron transport protein B / FeoB-type guanine nucleotide-binding (G) domain profile. / Nucleoside transporter/FeoB GTPase, Gate domain / Nucleoside recognition / GTP binding domain / Small GTP-binding protein domain / Helix Hairpins / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Ferrous iron transport protein B
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHattori, M. / Ishitani, R. / Nureki, O.
CitationJournal: Structure / Year: 2009
Title: Structural basis of novel interactions between the small-GTPase and GDI-like domains in prokaryotic FeoB iron transporter
Authors: Hattori, M. / Jin, Y. / Nishimasu, H. / Tanaka, Y. / Mochizuki, M. / Uchiumi, T. / Ishitani, R. / Ito, K. / Nureki, O.
History
DepositionApr 22, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Iron(II) transport protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6742
Polymers29,2311
Non-polymers4431
Water3,225179
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.152, 65.152, 104.798
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Iron(II) transport protein B


Mass: 29230.844 Da / Num. of mol.: 1 / Fragment: UNP residues 17-269
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0051 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q9WXQ8
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44 %
Crystal growpH: 8.5 / Details: 25% PEG3350, 0.1M Tris-HCl, pH8.5, 0.1M NaCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU
DetectorDate: Feb 28, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 31207

-
Processing

SoftwareName: PHENIX / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3A1S

3a1s


Resolution: 1.8→34.99 Å / SU ML: 0.54 / σ(F): 0.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2398 1199 5.02 %
Rwork0.1914 --
obs0.1939 23883 97.34 %
Solvent computationShrinkage radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.236 Å2 / ksol: 0.368 e/Å3
Refinement stepCycle: LAST / Resolution: 1.8→34.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2027 0 28 179 2234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072104
X-RAY DIFFRACTIONf_angle_d1.062879
X-RAY DIFFRACTIONf_dihedral_angle_d18.271786
X-RAY DIFFRACTIONf_chiral_restr0.068343
X-RAY DIFFRACTIONf_plane_restr0.004357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-1.87220.34481240.24912382X-RAY DIFFRACTION93
1.8722-1.95740.31231240.24012433X-RAY DIFFRACTION95
1.9574-2.06060.28841350.21632508X-RAY DIFFRACTION98
2.0606-2.18970.22891350.19762495X-RAY DIFFRACTION99
2.1897-2.35870.26131330.18552529X-RAY DIFFRACTION98
2.3587-2.5960.26861320.19542534X-RAY DIFFRACTION98
2.596-2.97150.25971370.19562586X-RAY DIFFRACTION99
2.9715-3.74310.20161380.17362609X-RAY DIFFRACTION100
3.7431-34.99630.21751410.17962608X-RAY DIFFRACTION95
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1refined1.8406-0.4539-0.32122.44140.07771.28550.03430.1742-0.03850.0866-0.23530.1756-0.0839-0.14150.140.34440.1033-0.07110.2861-0.06430.298226.47892.8043.2416
24.0641-0.2126-0.23520.5395-0.90551.84220.1921-0.60680.6981-0.10930.71920.16240.3701-0.4122-0.70790.43270.1063-0.09270.63040.02630.5728
3-0.0085-0.0829-0.06821.92460.47160.69930.10730.2759-0.4294-0.1351-0.25370.95430.2029-0.35110.19960.38810.0655-0.11290.4119-0.230.6718
40.90890.0212-0.31780.91410.8520.17950.16830.499-0.2005-0.3681-0.1844-0.21070.0702-0.0565-0.02150.39150.1461-0.0630.4165-0.07710.3305
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A 1-179
2X-RAY DIFFRACTION2chain A 180-189
3X-RAY DIFFRACTION3chain A 190-239
4X-RAY DIFFRACTION4chain A 240-268

+
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