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- PDB-7o1s: Complex-B bound [FeFe]-hydrogenase maturase HydE fromT. Maritima ... -

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Basic information

Entry
Database: PDB / ID: 7o1s
TitleComplex-B bound [FeFe]-hydrogenase maturase HydE fromT. Maritima (Wild-type protein)
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 / 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
CARBON MONOXIDE / CYANIDE ION / CYSTEINE / : / FE2/S2 (INORGANIC) CLUSTER / HYDROSULFURIC ACID / IODIDE ION / S-ADENOSYL-L-HOMOCYSTEINE / IRON/SULFUR CLUSTER / [FeFe] hydrogenase maturase subunit HydE
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 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)44,29817
Polymers39,8571
Non-polymers4,44016
Water6,431357
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-67 kcal/mol
Surface area14260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.270, 79.700, 86.110
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: 39857.277 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 , 11 types, 373 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-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#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-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#9: 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
#10: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#11: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 2.21 Å3/Da / Density % sol: 44.27 %
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: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.39→43.05 Å / Num. obs: 102006 / % possible obs: 99.3 % / Redundancy: 4.6 % / CC1/2: 0.998 / Net I/σ(I): 13.7
Reflection shellResolution: 1.39→1.48 Å / Num. unique obs: 2180 / CC1/2: 0.741

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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: 1.39→43.05 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.09 / Phase error: 22.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1804 5112 5.01 %
Rwork0.155 96894 -
obs0.1562 102006 74.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.43 Å2 / Biso mean: 26.3599 Å2 / Biso min: 12.75 Å2
Refinement stepCycle: final / Resolution: 1.39→43.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2727 0 252 357 3336
Biso mean--27.94 38.08 -
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 (%)
1.39-1.410.18120.331273752
1.41-1.430.506650.33293003057
1.43-1.440.3373320.360353656813
1.44-1.460.3123400.31691395321
1.46-1.480.3477560.27791209126528
1.48-1.50.4322730.27381553162636
1.5-1.520.27341100.26741841195143
1.52-1.540.25941060.26152176228250
1.54-1.570.25771320.25222494262658
1.57-1.590.29181430.24132868301166
1.59-1.620.27761690.22193153332273
1.62-1.650.23232070.21353506371381
1.65-1.680.22222120.19673678389087
1.68-1.720.25362190.18983974419392
1.72-1.750.19512210.18224228444997
1.75-1.80.20382400.18044223446399
1.8-1.840.21882470.169343064553100
1.84-1.890.19382090.162243834592100
1.89-1.950.17881880.168143094497100
1.95-2.010.19562330.156142994532100
2.01-2.080.18652220.148843174539100
2.08-2.160.17322420.145643494591100
2.16-2.260.17982780.146942394517100
2.26-2.380.17932520.144542704522100
2.38-2.530.18152370.150942874524100
2.53-2.730.16332480.15474282453099
2.73-30.17661870.15084304449199
3-3.430.1462130.15014293450699
3.43-4.320.15692010.12794284448599
4.33-43.050.16191880.1424247443598
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)
13.13090.1099-0.31693.77920.68492.7164-0.11190.1001-0.4559-0.5397-0.0414-0.34180.86270.56270.08980.54950.14790.08030.26490.02570.322557.8183-13.7644-3.3902
20.9106-0.3273-0.35580.80810.03971.1816-0.0053-0.1257-0.02880.04160.0246-0.0034-0.01580.0787-0.02290.1192-0.0328-0.0230.12660.00180.149544.21518.239812.464
31.6659-0.59640.40023.1066-2.23034.05010.0475-0.1483-0.01030.07430.09220.2118-0.088-0.1963-0.13840.1185-0.0165-0.00590.1096-0.01170.148930.541211.3116.0544
41.8166-0.90670.0451.711-0.41921.9215-0.057-0.1508-0.27260.00810.00050.1050.31380.04330.02680.1616-0.01760.0070.11440.03180.150436.3936-3.731117.2643
50.8345-0.0375-0.23130.6938-0.20211.4546-0.021-0.1327-0.1009-0.0054-0.0229-0.050.15430.17490.05050.13690.0088-0.01250.13420.01830.144649.6360.69919.0273
60.51560.125-0.72510.925-1.3063.5960.0655-0.2570.17040.2315-0.0377-0.0822-0.23040.3957-0.00210.2069-0.0304-0.02290.25-0.02170.203948.780917.737510.4527
72.6718-0.0235-0.53590.42611.00242.4417-0.03880.2604-0.19170.0016-0.05280.09380.4018-0.17370.07670.2294-0.0101-0.02580.1665-0.00380.197138.49723.1664-4.0802
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 28 )A1 - 28
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 98 )A29 - 98
3X-RAY DIFFRACTION3chain 'A' and (resid 99 through 129 )A99 - 129
4X-RAY DIFFRACTION4chain 'A' and (resid 130 through 189 )A130 - 189
5X-RAY DIFFRACTION5chain 'A' and (resid 190 through 299 )A190 - 299
6X-RAY DIFFRACTION6chain 'A' and (resid 300 through 329 )A300 - 329
7X-RAY DIFFRACTION7chain 'A' and (resid 330 through 401 )A330 - 401

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