[English] 日本語
Yorodumi
- PDB-5ff0: HydE from T. maritima in complex with S-adenosyl-L-cysteine and m... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ff0
TitleHydE from T. maritima in complex with S-adenosyl-L-cysteine and methionine
Components[FeFe] hydrogenase maturase subunit HydE
KeywordsOXIDOREDUCTASE / Radical SAM enzyme / complex / FeFe-hydrogenase maturase / thiazolidine
Function / homology
Function and homology information


water-soluble vitamin biosynthetic process / sulfur compound biosynthetic process / Oxidoreductases; Acting on a sulfur group of donors / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / transferase activity / oxidoreductase activity / metal ion binding
Similarity search - Function
Biotin and Thiamin Synthesis associated domain / [FeFe]-hydrogenase maturation HydE, radical SAM / HydE/PylB-like / Biotin and thiamin synthesis-associated domain / Biotin and Thiamin Synthesis associated domain / Elp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM ...Biotin and Thiamin Synthesis associated domain / [FeFe]-hydrogenase maturation HydE, radical SAM / HydE/PylB-like / Biotin and thiamin synthesis-associated domain / Biotin and Thiamin Synthesis associated domain / Elp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
S-adenosyl-L-cysteine / METHIONINE / Fe4-Se4 cluster / [FeFe] hydrogenase maturase subunit HydE
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsRohac, R. / Amara, P. / Benjdia, A. / Martin, L. / Ruffie, P. / Favier, A. / Berteau, O. / Mouesca, J.M. / Fontecilla-Camps, J.C. / Nicolet, Y.
CitationJournal: Nat.Chem. / Year: 2016
Title: Carbon-sulfur bond-forming reaction catalysed by the radical SAM enzyme HydE.
Authors: Rohac, R. / Amara, P. / Benjdia, A. / Martin, L. / Ruffie, P. / Favier, A. / Berteau, O. / Mouesca, J.M. / Fontecilla-Camps, J.C. / Nicolet, Y.
History
DepositionDec 17, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_validate_polymer_linkage
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_polymer_linkage.dist / _pdbx_validate_polymer_linkage.label_alt_id_1

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: [FeFe] hydrogenase maturase subunit HydE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,21311
Polymers41,0091
Non-polymers4,20410
Water8,989499
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-20 kcal/mol
Surface area14760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.890, 79.340, 86.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein [FeFe] hydrogenase maturase subunit HydE


Mass: 41009.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_1269, THEMA_07990, Tmari_1274 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9X0Z6, Oxidoreductases; Acting on a sulfur group of donors

-
Non-polymers , 6 types, 509 molecules

#2: Chemical ChemComp-SFS / Fe4-Se4 cluster


Mass: 539.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4Se4
#3: Chemical
ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS


Mass: 614.877 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#6: Chemical ChemComp-5X8 / S-adenosyl-L-cysteine


Type: L-peptide linking / Mass: 370.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H18N6O5S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG4000, Lithium sulfate, CHAPS, TrisHCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.49→44 Å / Num. obs: 57518 / % possible obs: 98.9 % / Redundancy: 3.8 % / Net I/σ(I): 13.73
Reflection shellResolution: 1.49→1.58 Å / Rsym value: 0.511

-
Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IIX

3iix


Resolution: 1.49→42.84 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.277 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16852 2898 5 %RANDOM
Rwork0.15032 ---
obs0.1512 54620 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.062 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å20 Å2
2--0.24 Å20 Å2
3----0.99 Å2
Refinement stepCycle: 1 / Resolution: 1.49→42.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2737 0 219 499 3455
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.023307
X-RAY DIFFRACTIONr_bond_other_d0.0030.023217
X-RAY DIFFRACTIONr_angle_refined_deg2.3272.0914576
X-RAY DIFFRACTIONr_angle_other_deg1.3333.0037464
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.035399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.32823.456136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4115550
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0391528
X-RAY DIFFRACTIONr_chiral_restr0.2120.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213567
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02694
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.811.71509
X-RAY DIFFRACTIONr_mcbond_other1.8081.71509
X-RAY DIFFRACTIONr_mcangle_it2.4122.5461919
X-RAY DIFFRACTIONr_mcangle_other2.4122.5461920
X-RAY DIFFRACTIONr_scbond_it2.8011.991798
X-RAY DIFFRACTIONr_scbond_other2.8011.991799
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0032.8922640
X-RAY DIFFRACTIONr_long_range_B_refined5.67117.8615111
X-RAY DIFFRACTIONr_long_range_B_other5.67117.8615108
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.491→1.529 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 216 -
Rwork0.251 3851 -
obs--96.93 %

+
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