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

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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 / 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

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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)44,58921
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

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Components

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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

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Non-polymers , 16 types, 390 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-PYR / PYRUVIC ACID


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


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


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


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


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


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


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


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


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


Mass: 18.015 Da / Num. of mol.: 370 / 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: 2.23 Å3/Da / Density % sol: 44.78 %
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: 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

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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: 1.34→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

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