[English] 日本語
Yorodumi
- PDB-1i7h: CRYSTAL STURCUTURE OF FDX -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 1i7h
TitleCRYSTAL STURCUTURE OF FDX
ComponentsFERREDOXIN
KeywordsELECTRON TRANSPORT / 2FE-2S / Electron transport
Function / homologyAdrenodoxin / 2Fe-2S ferredoxin-type iron-sulfur binding domain / Ferredoxin 2Fe-2S type, proteobacteria / Beta-grasp domain superfamily / Adrenodoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-like superfamily / 2Fe-2S iron-sulfur cluster binding domain / Adrenodoxin family, iron-sulfur binding region signature. / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / iron-sulfur cluster assembly ...Adrenodoxin / 2Fe-2S ferredoxin-type iron-sulfur binding domain / Ferredoxin 2Fe-2S type, proteobacteria / Beta-grasp domain superfamily / Adrenodoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-like superfamily / 2Fe-2S iron-sulfur cluster binding domain / Adrenodoxin family, iron-sulfur binding region signature. / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / iron-sulfur cluster assembly / 2 iron, 2 sulfur cluster binding / electron transfer activity / metal ion binding / cytosol / 2Fe-2S ferredoxin
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / 1.7 Å resolution
AuthorsKakuta, Y. / Horio, T. / Takahashi, Y. / Fukuyama, K.
CitationJournal: Biochemistry / Year: 2001
Title: Crystal structure of Escherichia coli Fdx, an adrenodoxin-type ferredoxin involved in the assembly of iron-sulfur clusters.
Authors: Kakuta, Y. / Horio, T. / Takahashi, Y. / Fukuyama, K.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 9, 2001 / Release: Mar 9, 2002
RevisionDateData content typeGroupProviderType
1.0Mar 9, 2002Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,5626
Polyers37,0343
Non-polymers5273
Water2,792155
1
A: FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5212
Polyers12,3451
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5212
Polyers12,3451
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5212
Polyers12,3451
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)107.501, 107.501, 85.682
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH 3

-
Components

#1: Protein/peptide FERREDOXIN /


Mass: 12344.811 Da / Num. of mol.: 3 / Source: (gene. exp.) Escherichia coli (E. coli) / Genus: Escherichia / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P0A9R4
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


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


Mass: 18.015 Da / Num. of mol.: 155 / Formula: H2O / Water

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.57 / Density percent sol: 52.17 %
Crystal grow
*PLUS
Temp: 23 ℃ / Method: vapor diffusion, hanging drop
components of the solutions
*PLUS

Crystal ID: 1

IDConcCommon nameSol IDDetailsChemical formula
120 mg/mlproteindrop
2100 mMTris-HClreservoirpH7.5
333 %PEG4000reservoir
45 %2-butanolreservoir
580 mMreservoirMgCl2

-
Data collection

DiffractionMean temperature: 140 kelvins
SourceSource: SYNCHROTRON / Type: SPRING-8 BEAMLINE BL41XU / Synchrotron site: SPring-8 / Beamline: BL41XU / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD
RadiationMonochromator: CRYSTAL / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 22 Å2 / D resolution high: 1.7 Å / D resolution low: 32.6 Å / Number obs: 155486 / Rmerge I obs: 0.066 / NetI over sigmaI: 6.4 / Redundancy: 3.9 % / Percent possible obs: 98.7
Reflection shellRmerge I obs: 0.273 / Highest resolution: 1.7 Å / Lowest resolution: 1.79 Å / MeanI over sigI obs: 1.2 / Number unique all: 5936 / Rsym value: 0.273 / Redundancy: 2.3 % / Percent possible all: 99.6
Reflection
*PLUS
D resolution low: 2 Å / Number obs: 40083 / Number measured all: 155486
Reflection shell
*PLUS
Percent possible obs: 99.6

+
Processing

Software
NameVersionClassification
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefineMethod to determine structure: MAD / R Free selection details: RANDOM / Data cutoff high absF: 1247563.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 2 / Stereochemistry target values: Engh & Huber
Solvent computationSolvent model details: FLAT MODEL / Solvent model param bsol: 49.49 / Solvent model param ksol: 0.427
Displacement parametersB iso mean: 28 Å2 / Aniso B11: -3.82 Å2 / Aniso B12: -0.69 Å2 / Aniso B13: 0 Å2 / Aniso B22: -3.82 Å2 / Aniso B23: 0 Å2 / Aniso B33: 7.64 Å2
Least-squares processR factor R free: 0.282 / R factor R free error: 0.003 / R factor R work: 0.262 / R factor obs: 0.264 / Highest resolution: 1.7 Å / Lowest resolution: 19.57 Å / Number reflection R free: 6834 / Number reflection obs: 71758 / Percent reflection R free: 9.5 / Percent reflection obs: 88.3
Refine analyzeLuzzati coordinate error free: 0.3 Å / Luzzati coordinate error obs: 0.27 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a free: 0.21 Å / Luzzati sigma a obs: 0.2 Å
Refine hist #LASTHighest resolution: 1.7 Å / Lowest resolution: 19.57 Å
Number of atoms included #LASTProtein: 2498 / Nucleic acid: 0 / Ligand: 12 / Solvent: 155 / Total: 2665
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.74
Refine LS shellHighest resolution: 1.7 Å / R factor R free: 0.337 / R factor R free error: 0.011 / R factor R work: 0.344 / Lowest resolution: 1.81 Å / Number reflection R free: 898 / Number reflection R work: 9019 / Total number of bins used: 6 / Percent reflection R free: 9.1 / Percent reflection obs: 73.4
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2FES.PARAMFES.TOP
X-RAY DIFFRACTION3WATER.PARAM
Refine
*PLUS
Sigma F: 2
Displacement parameters
*PLUS
B iso mean: 28 Å2
Least-squares process
*PLUS
R factor R free: 0.278 / R factor obs: 0.255 / Highest resolution: 1.7 Å / Lowest resolution: 2 Å / Percent reflection R free: 1
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74
Refine LS shell
*PLUS
Percent reflection R free: 9.1 / R factor R free: 0.337 / R factor R work: 0.344

+
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