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- PDB-7o26: Complex-B bound [FeFe]-hydrogenase maturase HydE fromT. Maritima ... -

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Basic information

Entry
Database: PDB / ID: 7o26
TitleComplex-B bound [FeFe]-hydrogenase maturase HydE fromT. Maritima (5'dA + Methionine)
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 / 2 iron, 2 sulfur cluster binding / transferase activity / 4 iron, 4 sulfur cluster binding / 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
5'-DEOXYADENOSINE / CARBON MONOXIDE / CYANIDE ION / CYSTEINE / : / FE2/S2 (INORGANIC) CLUSTER / HYDROSULFURIC ACID / IODIDE ION / METHIONINE / IRON/SULFUR CLUSTER / [FeFe] hydrogenase maturase subunit HydE
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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: Database references / Category: citation / citation_author / database_2
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 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,45720
Polymers39,8731
Non-polymers4,58419
Water6,107339
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-74 kcal/mol
Surface area14270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.880, 79.840, 86.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein [FeFe] hydrogenase maturase subunit HydE


Mass: 39873.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / 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

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Non-polymers , 14 types, 358 molecules

#2: Chemical ChemComp-CYS / 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


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


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#7: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2S
#8: Chemical ChemComp-5AD / 5'-DEOXYADENOSINE


Mass: 251.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O3 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#10: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#11: 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
#12: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#13: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#14: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG; LiSO4; Tris pH 7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.5→43.81 Å / Num. obs: 107892 / % possible obs: 99.5 % / Redundancy: 6.9 % / CC1/2: 0.988 / Net I/σ(I): 5.28
Reflection shellResolution: 1.5→1.59 Å / Num. unique obs: 8952 / CC1/2: 0.453

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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: 1.5→43.81 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.25 / Phase error: 23.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2165 5441 5.04 %
Rwork0.178 102451 -
obs0.1798 107892 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.91 Å2 / Biso mean: 25.9887 Å2 / Biso min: 10.48 Å2
Refinement stepCycle: final / Resolution: 1.5→43.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2746 0 260 341 3347
Biso mean--29.05 37.27 -
Num. residues----347
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 (%)
1.5-1.520.34251840.36973229341395
1.52-1.530.35881950.34883388358398
1.53-1.550.4051720.34093422359499
1.55-1.570.34521980.33613375357399
1.57-1.590.34791490.31343421357098
1.59-1.620.30681800.30153355353599
1.62-1.640.31451930.29743452364598
1.64-1.660.30792080.2933643572100
1.66-1.690.29151950.2763437363299
1.69-1.720.28891520.25893358351099
1.72-1.750.30681880.25323451363999
1.75-1.780.32742060.24573427363399
1.78-1.810.25521970.2343346354399
1.81-1.850.2661760.22043432360899
1.85-1.890.21021630.21243473363699
1.89-1.930.23361540.205134163570100
1.93-1.980.24961840.18553380356499
1.98-2.030.23911470.17113466361399
2.04-2.090.21072060.170234383644100
2.09-2.160.20491970.15833983595100
2.16-2.240.1881900.16234163606100
2.24-2.330.19592280.162334203648100
2.33-2.440.20681950.159934183613100
2.44-2.560.22961930.150734423635100
2.56-2.720.1941930.161334163609100
2.72-2.930.16821550.155334693624100
2.93-3.230.18851620.152134513613100
3.23-3.70.15481660.145234723638100
3.7-4.660.17121680.128834433611100
4.66-43.810.20671470.153634763623100
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)
14.1365-0.5961-0.42264.0206-0.39342.7897-0.16330.1404-0.5422-0.5206-0.0778-0.24640.82510.52580.16430.4740.11870.05270.23740.00490.298957.461-13.879-3.409
25.9509-2.62891.79162.8108-0.36643.27320.14980.2705-0.0439-0.2449-0.1188-0.090.23710.1418-0.02620.18060.01450.00790.1477-0.02050.157653.677-1.304-7.408
30.717-0.2629-0.60911.1859-0.2320.9789-0.0402-0.1930.02750.19850.0029-0.0269-0.08180.1360.05630.1242-0.0214-0.01910.1912-0.01280.15640.48411.58218.894
42.0018-0.53420.27433.3401-2.11583.74670.0589-0.19090.0310.12670.06930.235-0.118-0.1685-0.13160.1188-0.02190.00070.1304-0.01730.164330.29711.21816.248
51.9419-1.13570.19872.0368-0.59752.2124-0.0737-0.1587-0.24710.036-0.0080.15750.28480.0280.06080.1665-0.02060.01820.13630.02720.166835.969-3.69417.164
60.909-0.1402-0.21080.646-0.29761.7496-0.0258-0.1541-0.06180.019-0.0178-0.03160.14450.23540.03580.13960.0113-0.01360.15940.01150.164349.5040.8499.071
70.33990.2224-0.72480.8024-0.83293.37870.0655-0.24020.18780.1641-0.0103-0.1434-0.1740.5446-0.01970.1684-0.0279-0.02170.2568-0.03340.214748.35217.83110.102
83.4167-0.4207-0.94090.98880.11862.1496-0.05760.1807-0.2096-0.0673-0.02850.15910.4018-0.08290.05890.1982-0.0246-0.03150.1775-0.02010.1738.2443.156-4.064
95.29572.59164.84892.02862.30744.4514-0.4430.5216-0.49430.18140.6593-0.52720.6871-0.2519-0.23480.4823-0.1508-0.08310.41340.01910.37942.0053.0619.671
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:28 )A1 - 28
2X-RAY DIFFRACTION2( CHAIN A AND RESID 29:47 )A29 - 47
3X-RAY DIFFRACTION3( CHAIN A AND RESID 48:98 )A48 - 98
4X-RAY DIFFRACTION4( CHAIN A AND RESID 99:129 )A99 - 129
5X-RAY DIFFRACTION5( CHAIN A AND RESID 130:189 )A130 - 189
6X-RAY DIFFRACTION6( CHAIN A AND RESID 190:299 )A190 - 299
7X-RAY DIFFRACTION7( CHAIN A AND RESID 300:329 )A300 - 329
8X-RAY DIFFRACTION8( CHAIN A AND ( RESID 330:347 OR RESID 401:401 ) )A330 - 347
9X-RAY DIFFRACTION8( CHAIN A AND ( RESID 330:347 OR RESID 401:401 ) )A401
10X-RAY DIFFRACTION9( CHAIN A AND RESID 406:406 )A406

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