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- PDB-7o1p: [FeFe]-hydrogenase maturase HydE from T. Maritima (C-ter stretch ... -

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Basic information

Entry
Database: PDB / ID: 7o1p
Title[FeFe]-hydrogenase maturase HydE from T. Maritima (C-ter stretch absent)
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
CARBONATE 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: 2.58 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)43,70312
Polymers39,7261
Non-polymers3,97711
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-49 kcal/mol
Surface area14540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.450, 79.160, 85.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 39726.082 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 , 6 types, 20 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: 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
#4: 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
#5: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.23 Å3/Da / Density % sol: 44.93 %
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: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.58→40 Å / Num. obs: 11701 / % possible obs: 99.5 % / Redundancy: 3.8 % / CC1/2: 0.999 / Net I/σ(I): 17.52
Reflection shellResolution: 2.58→2.74 Å / Num. unique obs: 1501 / CC1/2: 0.704

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CIW

3ciw


Resolution: 2.58→40 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.28 / Phase error: 25.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2404 990 4.58 %
Rwork0.1793 --
obs0.1818 11701 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.58→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2606 0 208 9 2823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032984
X-RAY DIFFRACTIONf_angle_d1.1014117
X-RAY DIFFRACTIONf_dihedral_angle_d19.3961236
X-RAY DIFFRACTIONf_chiral_restr0.057500
X-RAY DIFFRACTIONf_plane_restr0.005488
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.58-2.720.33141640.26372894X-RAY DIFFRACTION98
2.72-2.890.26571370.22542959X-RAY DIFFRACTION100
2.89-3.110.32131520.22052928X-RAY DIFFRACTION100
3.11-3.420.30041370.20662964X-RAY DIFFRACTION100
3.42-3.920.20731380.17732953X-RAY DIFFRACTION100
3.92-4.930.16991290.14712958X-RAY DIFFRACTION100
4.94-400.25291330.16972947X-RAY DIFFRACTION99
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)
12.57-0.6219-0.41321.6210.35590.9997-0.36530.13230.0222-1.00190.2715-0.76180.6576-0.0652-0.02650.99770.05210.15920.5786-0.00550.652658.085-7.776-5.262
21.9412-0.8712-0.27283.00870.4932.5796-0.1087-0.2351-0.23730.22090.18250.40.1724-0.0688-0.0030.4534-0.01420.010.53760.11470.505536.7747.18516.854
31.5841-1.16990.73441.1095-1.08741.5304-0.1553-1.5785-0.95210.06130.11790.11120.9071-0.7153-0.12820.7636-0.08-0.01830.64680.16930.910542.213-10.14318.722
41.1471-0.3423-1.18171.7632-0.49531.9954-0.3711-0.391-0.2142-0.00150.0317-0.16720.60690.1461-0.04870.75580.0146-0.02450.60850.07240.714450.903-4.39812.27
51.27870.1377-1.49381.7851-0.45881.79-0.1551-0.18250.0643-0.2202-0.0611-0.19280.2348-0.1370.00410.40990.0042-0.0460.48030.00330.490251.7345.344.37
60.2166-0.00080.1040.46210.34060.35810.0639-0.09930.2002-0.0199-0.0442-0.2349-0.03710.4118-0.00770.61090.01110.01410.6786-0.01740.597549.44217.2048.554
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:47 )A2 - 47
2X-RAY DIFFRACTION2( CHAIN A AND RESID 48:164 )A48 - 164
3X-RAY DIFFRACTION3( CHAIN A AND RESID 165:189 )A165 - 189
4X-RAY DIFFRACTION4( CHAIN A AND RESID 190:245 )A190 - 245
5X-RAY DIFFRACTION5( CHAIN A AND RESID 246:298 )A246 - 298
6X-RAY DIFFRACTION6( CHAIN A AND RESID 299:334 )A299 - 334

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