[English] 日本語
Yorodumi
- PDB-4xdd: Apo [FeFe]-Hydrogenase CpI -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xdd
TitleApo [FeFe]-Hydrogenase CpI
ComponentsIron hydrogenase 1
KeywordsOXIDOREDUCTASE / CpI / FeFe-Hydrogenase
Function / homology
Function and homology information


ferredoxin hydrogenase / ferredoxin hydrogenase activity / 4 iron, 4 sulfur cluster binding / iron ion binding
Similarity search - Function
Ubiquitin-like (UB roll) - #740 / Iron hydrogenase, small subunit superfamily / Iron hydrogenase, subset / Iron hydrogenase, small subunit / Iron hydrogenase small subunit / Iron hydrogenase small subunit / Iron hydrogenase / Iron only hydrogenase large subunit, C-terminal domain / Iron hydrogenase, large subunit, C-terminal / 2Fe-2S iron-sulfur cluster binding domain ...Ubiquitin-like (UB roll) - #740 / Iron hydrogenase, small subunit superfamily / Iron hydrogenase, subset / Iron hydrogenase, small subunit / Iron hydrogenase small subunit / Iron hydrogenase small subunit / Iron hydrogenase / Iron only hydrogenase large subunit, C-terminal domain / Iron hydrogenase, large subunit, C-terminal / 2Fe-2S iron-sulfur cluster binding domain / Alpha-Beta Plaits - #20 / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / 4Fe-4S dicluster domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Ubiquitin-like (UB roll) / Alpha-Beta Plaits / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / IRON/SULFUR CLUSTER / Iron hydrogenase 1
Similarity search - Component
Biological speciesClostridium pasteurianum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.599 Å
AuthorsEsselborn, J. / Hofmann, E. / Kurisu, G. / Happe, T.
CitationJournal: Chem Sci / Year: 2016
Title: A structural view of synthetic cofactor integration into [FeFe]-hydrogenases.
Authors: Esselborn, J. / Muraki, N. / Klein, K. / Engelbrecht, V. / Metzler-Nolte, N. / Apfel, U.P. / Hofmann, E. / Kurisu, G. / Happe, T.
History
DepositionDec 19, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Iron hydrogenase 1
B: Iron hydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,64523
Polymers129,9652
Non-polymers3,68021
Water25,2211400
1
A: Iron hydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,77611
Polymers64,9821
Non-polymers1,79410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Iron hydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,86812
Polymers64,9821
Non-polymers1,88611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.057, 71.807, 103.308
Angle α, β, γ (deg.)90.00, 97.93, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.774151, 0.585773, 0.239917), (0.584472, -0.80701, 0.084427), (0.243071, 0.074866, -0.967115)-19.21785, 43.46664, 37.98365

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Iron hydrogenase 1 / CpI / Fe-only hydrogenase / [Fe] hydrogenase


Mass: 64982.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium pasteurianum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P29166, ferredoxin hydrogenase

-
Non-polymers , 6 types, 1421 molecules

#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1400 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG4000, MgCl / PH range: 7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.599→50 Å / Num. obs: 172056 / % possible obs: 99.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 36.8
Reflection shellResolution: 1.599→1.63 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 3.2 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C8Y
Resolution: 1.599→38.963 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1658 8589 5.01 %RANDOM
Rwork0.1438 ---
obs0.1449 171439 99.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.599→38.963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9139 0 0 1400 10539
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069372
X-RAY DIFFRACTIONf_angle_d0.95212621
X-RAY DIFFRACTIONf_dihedral_angle_d13.4953487
X-RAY DIFFRACTIONf_chiral_restr0.0361373
X-RAY DIFFRACTIONf_plane_restr0.0041629
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5995-1.61770.27212680.25265261X-RAY DIFFRACTION97
1.6177-1.63670.27822870.24275435X-RAY DIFFRACTION100
1.6367-1.65670.26552980.22725368X-RAY DIFFRACTION100
1.6567-1.67760.22362510.22125445X-RAY DIFFRACTION100
1.6776-1.69970.25042580.21215451X-RAY DIFFRACTION100
1.6997-1.7230.24342660.20285387X-RAY DIFFRACTION100
1.723-1.74760.2262930.19225448X-RAY DIFFRACTION100
1.7476-1.77370.20262620.1855398X-RAY DIFFRACTION100
1.7737-1.80140.21022870.17925442X-RAY DIFFRACTION100
1.8014-1.83090.19792690.17255393X-RAY DIFFRACTION100
1.8309-1.86250.1913010.16475404X-RAY DIFFRACTION100
1.8625-1.89640.18382990.16085432X-RAY DIFFRACTION100
1.8964-1.93280.19993020.15985397X-RAY DIFFRACTION100
1.9328-1.97230.19392920.15445427X-RAY DIFFRACTION100
1.9723-2.01520.17122760.14755435X-RAY DIFFRACTION100
2.0152-2.06210.16142850.14545504X-RAY DIFFRACTION100
2.0621-2.11360.16362990.14225388X-RAY DIFFRACTION100
2.1136-2.17080.1642900.13925440X-RAY DIFFRACTION100
2.1708-2.23460.17833010.14065410X-RAY DIFFRACTION100
2.2346-2.30670.16623010.13235431X-RAY DIFFRACTION100
2.3067-2.38920.15812740.13285485X-RAY DIFFRACTION100
2.3892-2.48480.16423020.14015406X-RAY DIFFRACTION100
2.4848-2.59790.17042870.13945454X-RAY DIFFRACTION100
2.5979-2.73480.15742940.1425476X-RAY DIFFRACTION100
2.7348-2.90610.18782880.14635446X-RAY DIFFRACTION100
2.9061-3.13040.16632710.14475494X-RAY DIFFRACTION100
3.1304-3.44530.15673170.13815435X-RAY DIFFRACTION100
3.4453-3.94340.14642910.12485502X-RAY DIFFRACTION100
3.9434-4.96670.13082820.1155478X-RAY DIFFRACTION99
4.9667-38.97450.14762980.14165378X-RAY DIFFRACTION95

+
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