[English] 日本語
Yorodumi
- PDB-1frd: MOLECULAR STRUCTURE OF THE OXIDIZED, RECOMBINANT, HETEROCYST (2FE... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 1frd
TitleMOLECULAR STRUCTURE OF THE OXIDIZED, RECOMBINANT, HETEROCYST (2FE-2S) FERREDOXIN FROM ANABAENA 7120 DETERMINED TO 1.7 ANGSTROMS RESOLUTION
ComponentsHETEROCYST [2FE-2S] FERREDOXIN
KeywordsELECTRON TRANSPORT
Function / homology2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 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. / heterocyst differentiation / nitrogen fixation ...2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 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. / heterocyst differentiation / nitrogen fixation / 2 iron, 2 sulfur cluster binding / electron transfer activity / metal ion binding / Ferredoxin, heterocyst
Function and homology information
Specimen sourceNostoc sp. (Cyanobacteria)
MethodX-RAY DIFFRACTION / 1.7 Å resolution
AuthorsJacobson, B.L. / Chae, Y.K. / Markley, J.L. / Rayment, I. / Holden, H.M.
CitationJournal: Biochemistry / Year: 1993
Title: Molecular structure of the oxidized, recombinant, heterocyst [2Fe-2S] ferredoxin from Anabaena 7120 determined to 1.7-A resolution.
Authors: Jacobson, B.L. / Chae, Y.K. / Markley, J.L. / Rayment, I. / Holden, H.M.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 14, 1993 / Release: May 31, 1994
RevisionDateData content typeGroupProviderType
1.0May 31, 1994Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelSource and taxonomy / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HETEROCYST [2FE-2S] FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0032
Polyers10,8271
Non-polymers1761
Water1,04558
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)44.200, 44.200, 80.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP 65

-
Components

#1: Protein/peptide HETEROCYST [2FE-2S] FERREDOXIN


Mass: 10826.987 Da / Num. of mol.: 1 / Source: (gene. exp.) Nostoc sp. (Cyanobacteria) / Genus: Nostoc / Strain: PCC 7120 / References: UniProt: P11053
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Formula: Fe2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Formula: H2O / Water

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.1 / Density percent sol: 41.39 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Details: referred to 'Jacobson, B.L.', (1992) Arch. Biochem. Biophys., 294, 279-281
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDDetails
120 mg/mlprotein1drop
250 mMbis-Tris propane1reservoirpH7.0
3ammonium sulfate1reservoirpH4.5-9.0
4PEG80001reservoir

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
D resolution high: 1.68 Å / D resolution low: 9999 Å / Percent possible obs: 99

-
Processing

SoftwareName: TNT / Classification: refinement
Least-squares processR factor obs: 0.167 / Highest resolution: 1.7 Å / Lowest resolution: 3 Å / Number reflection obs: 9743
Refine hist #LASTHighest resolution: 1.7 Å / Lowest resolution: 3 Å
Number of atoms included #LASTProtein: 755 / Nucleic acid: 0 / Ligand: 4 / Solvent: 58 / Total: 817
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.009
X-RAY DIFFRACTIONt_angle_deg2.93
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Least-squares process
*PLUS
R factor obs: 0.167
Refine LS restraints
*PLUS
Refine IDType
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg

+
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