[English] 日本語
Yorodumi
- PDB-1fxi: STRUCTURE OF THE [2FE-2S] FERREDOXIN I FROM THE BLUE-GREEN ALGA A... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 1fxi
TitleSTRUCTURE OF THE [2FE-2S] FERREDOXIN I FROM THE BLUE-GREEN ALGA APHANOTHECE SACRUM AT 2.2 ANGSTROMS RESOLUTION
ComponentsFERREDOXIN I
KeywordsELECTRON TRANSFER (IRON-SULFUR PROTEIN)
Function / homology2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin, iron-sulphur binding site / Ferredoxin [2Fe-2S], plant / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-like superfamily / 2Fe-2S iron-sulfur cluster binding domain / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2 iron, 2 sulfur cluster binding / electron transfer activity ...2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin, iron-sulphur binding site / Ferredoxin [2Fe-2S], plant / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-like superfamily / 2Fe-2S iron-sulfur cluster binding domain / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2 iron, 2 sulfur cluster binding / electron transfer activity / metal ion binding / Ferredoxin-1
Function and homology information
Specimen sourceAphanothece sacrum (Cyanobacteria)
MethodX-RAY DIFFRACTION / 2.2 Å resolution
AuthorsTsukihara, T.
Citation
Journal: J.Mol.Biol. / Year: 1990
Title: Structure of the [2Fe-2S] ferredoxin I from the blue-green alga Aphanothece sacrum at 2.2 A resolution.
Authors: Tsukihara, T. / Fukuyama, K. / Mizushima, M. / Harioka, T. / Kusunoki, M. / Katsube, Y. / Hase, T. / Matsubara, H.
#1: Journal: J.Biochem.(Tokyo) / Year: 1983
Title: Main Chain Fold of a [2Fe-2S] Ferredoxin I from Aphanothece Sacrum at 2.5 Angstroms Resolution
Authors: Tsutsui, T. / Tsukihara, T. / Fukuyama, K. / Katsube, Y. / Hase, T. / Matsubara, H. / Nishikawa, Y. / Tanaka, N.
#2: Journal: J.Biochem.(Tokyo) / Year: 1978
Title: Crystallization and a 5 Angstroms X-Ray Diffraction Study of Aphanothece Sacrum Ferredoxin
Authors: Kunita, A. / Koshibe, M. / Nishikawa, Y. / Fukuyama, K. / Tsukihara, T. / Katsube, Y. / Matsuura, Y. / Tanaka, N. / Kakudo, M. / Hase, T. / Matsubara, H.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 28, 1990 / Release: Oct 15, 1991
RevisionDateData content typeGroupProviderType
1.0Oct 15, 1991Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FERREDOXIN I
B: FERREDOXIN I
C: FERREDOXIN I
D: FERREDOXIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9608
Polyers41,2574
Non-polymers7034
Water2,846158
1
A: FERREDOXIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4902
Polyers10,3141
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FERREDOXIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4902
Polyers10,3141
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: FERREDOXIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4902
Polyers10,3141
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: FERREDOXIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4902
Polyers10,3141
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)92.200, 92.200, 47.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP 41

-
Components

#1: Protein/peptide
FERREDOXIN I /


Mass: 10314.291 Da / Num. of mol.: 4 / Source: (gene. exp.) Aphanothece sacrum (Cyanobacteria) / Genus: Aphanothece / References: UniProt: P00250
#2: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Formula: Fe2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Formula: H2O / Water

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.45 / Density percent sol: 49.81 %
Crystal grow
*PLUS
Temp: 4 ℃ / Method: microdialysis / Details: Kunita, A., (1978) J.Biochem.(Tokyo), 84, 989.
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
11-3 %protein solution11
275 %satammonium sulfate12
30.7 M12NaCl
40.1 MTris-HCl12

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Number obs: 21790 / Number measured all: 42249

-
Processing

SoftwareName: PROLSQ / Classification: refinement
RefineSigma F: 2
Least-squares processR factor obs: 0.23 / Highest resolution: 2.2 Å / Lowest resolution: 6 Å / Number reflection obs: 13487
Refine hist #LASTHighest resolution: 2.2 Å / Lowest resolution: 6 Å
Number of atoms included #LASTProtein: 2884 / Nucleic acid: 0 / Ligand: 16 / Solvent: 158 / Total: 3058
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.020
X-RAY DIFFRACTIONp_angle_d0.0740.040
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0820.050
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.262.000
X-RAY DIFFRACTIONp_mcangle_it4.013.000
X-RAY DIFFRACTIONp_scbond_it4.053.000
X-RAY DIFFRACTIONp_scangle_it4.564.000
X-RAY DIFFRACTIONp_plane_restr0.0210.020
X-RAY DIFFRACTIONp_chiral_restr0.1890.150
X-RAY DIFFRACTIONp_singtor_nbd0.2960.500
X-RAY DIFFRACTIONp_multtor_nbd0.4200.500
X-RAY DIFFRACTIONp_xhyhbond_nbd0.4210.500
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.63.0
X-RAY DIFFRACTIONp_staggered_tor29.015.0
X-RAY DIFFRACTIONp_orthonormal_tor41.220.0
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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