[English] 日本語
Yorodumi
- PDB-7o25: Complex-B bound [FeFe]-hydrogenase maturase HydE from T. maritima... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7o25
TitleComplex-B bound [FeFe]-hydrogenase maturase HydE from T. maritima (reaction triggered in the crystal)
Components[FeFe] hydrogenase maturase subunit HydE
KeywordsMETAL BINDING PROTEIN / Radical SAM protein / Hydrogenase maturase / metalloprotein
Function / homology
Function and homology information


water-soluble vitamin biosynthetic process / : / sulfur compound biosynthetic process / : / Oxidoreductases; Acting on a sulfur group of donors / : / organonitrogen compound biosynthetic process / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / transferase activity ...water-soluble vitamin biosynthetic process / : / sulfur compound biosynthetic process / : / Oxidoreductases; Acting on a sulfur group of donors / : / organonitrogen compound biosynthetic process / 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 / Aldolase-type TIM barrel
Similarity search - Domain/homology
S-adenosyl-L-cysteine / CARBON MONOXIDE / CYANIDE ION / CYSTEINE / : / METHIONINE / PHOSPHATE ION / PYRUVIC ACID / S-ADENOSYLMETHIONINE / IRON/SULFUR CLUSTER / [FeFe] hydrogenase maturase subunit HydE
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsRohac, R. / Martin, L. / Liu, L. / Basu, D. / Tao, L. / Britt, R.D. / Rauchfuss, T. / Nicolet, Y.
Funding support France, United States, 3items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-15-IDEX-02 France
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1R35GM126961 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)GM-61153 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Crystal Structure of the [FeFe]-Hydrogenase Maturase HydE Bound to Complex-B.
Authors: Rohac, R. / Martin, L. / Liu, L. / Basu, D. / Tao, L. / Britt, R.D. / Rauchfuss, T.B. / Nicolet, Y.
History
DepositionMar 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 18, 2021Group: Advisory / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id
Revision 2.1Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
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)44,58921
Polymers41,0091
Non-polymers3,57920
Water6,666370
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-68 kcal/mol
Surface area15200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.410, 81.700, 70.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
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 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9X0Z6, Oxidoreductases; Acting on a sulfur group of donors

-
Non-polymers , 16 types, 390 molecules

#2: Chemical ChemComp-CYS / CYSTEINE / Cysteine


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CMO / CARBON MONOXIDE / Carbon monoxide


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CYN / CYANIDE ION / Cyanide


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PYR / PYRUVIC ACID / Pyruvic acid


Mass: 88.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O3
#7: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#8: Chemical ChemComp-MET / METHIONINE / Methionine


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#10: Chemical ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS / CHAPS detergent


Mass: 614.877 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#11: 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 / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE / Tris


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#13: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#14: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#15: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#16: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#17: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG; LiSO4; Tris pH 7.4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9805 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9805 Å / Relative weight: 1
ReflectionResolution: 1.34→47.15 Å / Num. obs: 159228 / % possible obs: 99.6 % / Redundancy: 14.4 % / CC1/2: 0.999 / Net I/σ(I): 14.8
Reflection shellResolution: 1.34→1.42 Å / Num. unique obs: 12982 / CC1/2: 0.729

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CIW

3ciw


Resolution: 1.34→47.15 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 17.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.166 7937 4.98 %
Rwork0.1448 151291 -
obs0.1459 159228 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.09 Å2 / Biso mean: 23.3075 Å2 / Biso min: 9.53 Å2
Refinement stepCycle: final / Resolution: 1.34→47.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2843 0 196 374 3413
Biso mean--32.4 36.19 -
Num. residues----356
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.34-1.350.35882180.36644170438882
1.35-1.370.2922670.292750845351100
1.37-1.380.27322530.282451105363100
1.38-1.40.29512760.27950815357100
1.4-1.420.26232600.260950625322100
1.42-1.440.26582730.240450795352100
1.44-1.460.26162600.227250655325100
1.46-1.480.23012580.205850745332100
1.48-1.510.20742710.189750875358100
1.51-1.530.19532660.178850545320100
1.53-1.560.1842600.177350525312100
1.56-1.590.20272720.167751195391100
1.59-1.620.20492620.160950385300100
1.62-1.650.1792640.153450775341100
1.65-1.680.17742730.149550915364100
1.68-1.720.19172720.140550265298100
1.72-1.770.14912610.138651095370100
1.77-1.810.16192780.137350945372100
1.81-1.870.17492630.13350365299100
1.87-1.930.14142680.133550675335100
1.93-20.16152650.132350435308100
2-2.080.1552670.130750795346100
2.08-2.170.15742600.128950725332100
2.17-2.290.15292650.127550825347100
2.29-2.430.14242700.133150935363100
2.43-2.620.17782660.142950665332100
2.62-2.880.16752620.138550655327100
2.88-3.30.14332670.132750855352100
3.3-4.150.13522710.119950705341100
4.15-47.150.16032690.138550615330100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.1508-1.7741-4.06222.00560.46735.4909-0.01910.18860.1895-0.24460.08090.03970.06980.3171-0.17220.1739-0.0564-0.06950.26490.04690.328724.16914.291-20.88
23.1145-0.942-1.63361.25390.97554.46520.07270.02840.2210.0312-0.018-0.2544-0.04180.2411-0.00580.0876-0.0175-0.0120.1520.03510.198610.52115.188-13.897
30.7409-0.1298-0.00950.64340.01841.2901-0.0040.00160.00070.00210.00730.0604-0.0262-0.18270.00920.13120.00320.00150.13810.00470.1356-23.47615.716-18.246
41.8602-0.3159-1.25780.66690.32753.23560.03580.06310.1513-0.0966-0.0311-0.0321-0.22150.03550.00140.15110.0057-0.00190.08970.01910.1322-14.26325.514-25.147
50.7258-0.18210.10180.4528-0.02030.68010.04570.06050.0624-0.0831-0.0676-0.073-0.03670.05680.02750.17570.00190.00750.14220.01510.1694-2.82516.033-21.66
61.3854-0.01020.23090.4482-0.22120.46030.00410.0267-0.1238-0.0281-0.00330.0160.0927-0.0528-0.00610.1691-0.0093-0.00190.1576-0.00460.1765-14.15.74-14.146
72.64030.41310.20382.58080.32481.48910.0089-0.26410.01320.1549-0.0054-0.0738-0.02260.0507-0.00170.16540.0202-0.00230.1986-0.01190.1337-9.39214.849-2.982
87.51431.65994.35085.7291-4.42977.9423-0.79560.00010.13930.68330.5165-2.352-0.9979-0.19010.3370.2719-0.01280.02970.2989-0.14570.3232-16.28216.494-25.011
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID -9:11 )A-9 - 11
2X-RAY DIFFRACTION2( CHAIN A AND RESID 12:46 )A12 - 46
3X-RAY DIFFRACTION3( CHAIN A AND RESID 47:129 )A47 - 129
4X-RAY DIFFRACTION4( CHAIN A AND RESID 130:189 )A130 - 189
5X-RAY DIFFRACTION5( CHAIN A AND RESID 190:268 )A190 - 268
6X-RAY DIFFRACTION6( CHAIN A AND RESID 269:317 )A269 - 317
7X-RAY DIFFRACTION7( CHAIN A AND ( RESID 318:346 OR RESID 401:401 ) )A318 - 346
8X-RAY DIFFRACTION7( CHAIN A AND ( RESID 318:346 OR RESID 401:401 ) )A401
9X-RAY DIFFRACTION8( CHAIN A AND RESID 408:408 )A408

+
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