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- PDB-8qml: (2R,4R)-MeTDA bound HydE structure (control experiment) -

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Basic information

Entry
Database: PDB / ID: 8qml
Title(2R,4R)-MeTDA bound HydE structure (control experiment)
Components[FeFe] hydrogenase maturase subunit HydE
KeywordsMETAL BINDING PROTEIN / [FeFe]-hydrogenase / radical SAM enzyme / HydE / Maturase / Complex-B / H-cluster
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
[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
Chem-41K / S-ADENOSYL-L-HOMOCYSTEINE / IRON/SULFUR CLUSTER / [FeFe] hydrogenase maturase subunit HydE
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsOmeiri, J. / Martin, L. / Usclat, A. / Cherrier, M.V. / Nicolet, Y.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-15-IDEX-02 France
Agence Nationale de la Recherche (ANR)ANR-17-EURE-0003 France
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: Maturation of the [FeFe]-Hydrogenase: Direct Transfer of the ( kappa 3 -cysteinate)Fe II (CN)(CO) 2 Complex B from HydG to HydE.
Authors: Omeiri, J. / Martin, L. / Usclat, A. / Cherrier, M.V. / Nicolet, Y.
History
DepositionSep 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 20, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Dec 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)45,15911
Polymers41,0251
Non-polymers4,13310
Water5,837324
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-41 kcal/mol
Surface area14100 Å2
Unit cell
Length a, b, c (Å)50.480, 79.220, 85.160
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein [FeFe] hydrogenase maturase subunit HydE


Mass: 41025.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Gene: TM_1269, THEMA_07990, Tmari_1274 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9X0Z6, Oxidoreductases; Acting on a sulfur group of donors

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Non-polymers , 7 types, 334 molecules

#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-41K / (2R,4R)-2-methyl-1,3-thiazolidine-2,4-dicarboxylic acid


Mass: 191.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H9NO4S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS / CHAPS detergent


Mass: 614.877 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#5: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.08 Å3/Da / Density % sol: 40.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 4000; Tris pH=8; LiSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM07 / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.4→40 Å / Num. obs: 129324 / % possible obs: 99.9 % / Redundancy: 5.1 % / Biso Wilson estimate: 21.07 Å2 / CC1/2: 0.997 / Net I/σ(I): 14.75
Reflection shellResolution: 1.4→1.44 Å / Num. unique obs: 9533 / CC1/2: 0.483

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→23.14 Å / SU ML: 0.1793 / Cross valid method: FREE R-VALUE / σ(F): 1.23 / Phase error: 24.2773
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1925 6373 4.93 %
Rwork0.154 122951 -
obs0.1559 129324 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.51 Å2
Refinement stepCycle: LAST / Resolution: 1.4→23.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2720 0 215 324 3259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01383543
X-RAY DIFFRACTIONf_angle_d1.78834955
X-RAY DIFFRACTIONf_chiral_restr0.1209589
X-RAY DIFFRACTIONf_plane_restr0.0179607
X-RAY DIFFRACTIONf_dihedral_angle_d19.61721537
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.32712140.35553986X-RAY DIFFRACTION98.36
1.42-1.430.45912200.37124128X-RAY DIFFRACTION99.38
1.43-1.450.37541930.35634066X-RAY DIFFRACTION99.49
1.45-1.470.36492000.33724154X-RAY DIFFRACTION99.41
1.47-1.490.32190.29094077X-RAY DIFFRACTION99.72
1.49-1.510.30362190.28514094X-RAY DIFFRACTION99.77
1.51-1.530.28312100.25624138X-RAY DIFFRACTION99.61
1.53-1.550.21332170.23834075X-RAY DIFFRACTION99.67
1.55-1.580.28011980.22294118X-RAY DIFFRACTION99.81
1.58-1.60.26552230.23024073X-RAY DIFFRACTION99.72
1.6-1.630.27072100.25414128X-RAY DIFFRACTION99.7
1.63-1.660.2732020.23384067X-RAY DIFFRACTION99.44
1.66-1.690.33462140.28774043X-RAY DIFFRACTION96.88
1.69-1.730.19812130.19074046X-RAY DIFFRACTION99.88
1.73-1.760.19762200.16774141X-RAY DIFFRACTION99.93
1.76-1.810.19232190.1654101X-RAY DIFFRACTION99.93
1.81-1.850.23982080.1514121X-RAY DIFFRACTION99.79
1.85-1.90.22162190.15934061X-RAY DIFFRACTION99.74
1.9-1.960.18092060.15574145X-RAY DIFFRACTION99.86
1.96-2.020.20482210.14854129X-RAY DIFFRACTION99.91
2.02-2.090.17322190.14314060X-RAY DIFFRACTION99.51
2.09-2.170.19542110.13954112X-RAY DIFFRACTION99.88
2.18-2.270.16442100.14674118X-RAY DIFFRACTION99.86
2.27-2.390.2022150.13894116X-RAY DIFFRACTION100
2.39-2.540.21422180.15094111X-RAY DIFFRACTION99.98
2.54-2.740.19432240.15194094X-RAY DIFFRACTION99.88
2.74-3.010.17672200.14674096X-RAY DIFFRACTION99.72
3.01-3.450.17172160.13124107X-RAY DIFFRACTION99.88
3.45-4.340.13882030.1114117X-RAY DIFFRACTION99.86
4.34-23.140.16691920.13094129X-RAY DIFFRACTION99.65
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)
13.91621603921.46428567924-0.3348981077773.85806917520.8587309144274.68479121179-0.36147447671-0.166196965344-0.736745033337-0.4945898276610.135673251095-0.3277708608090.9398330254440.4005187579350.2216161119190.5148803030960.1305168668480.1033124175030.2539012114870.02824329199180.39476201906756.7107869084-13.5440255203-2.78713323243
26.34222005015-1.73125675229-0.921601988992.15365013630.2521087777053.958160940860.04841545922920.22963888231-0.0528772138301-0.227708466014-0.0563673670616-0.1057758750930.151279277140.008039112091690.1023181559070.231829139190.01152137991470.01166942902770.14867587561-0.02175666067550.19822831711953.1949757708-0.91103275801-7.63707019336
31.14834466554-0.0216957441685-0.5334278288941.07167382421-0.2724025705371.974091019120.0133237301828-0.241847925534-0.03789110441060.120106022595-0.003534517721820.0752174487124-0.0103574938520.1096792640040.001736307118350.137336952648-0.0215425139219-0.00270741670690.1822931603090.006118366275660.13569122846734.83272364258.3091252428716.9478711422
42.33330699799-1.207090241520.4915355034491.33567042749-0.5039643732353.0330439092-0.175490028177-0.475599344307-0.5140286584390.1148536502760.01797029564590.1159646021760.6666775190820.2734664924580.04762255953880.3451318380320.04634715474720.05973211419120.2629195354980.1157709531690.29696470983339.78628613-9.4701912347119.1587109121
51.19522504958-0.0244461119037-0.67152046810.743883011642-0.1391947127531.50532312883-0.0344699745154-0.271958030937-0.1196081370760.0453809662901-0.0157288812095-0.08098272061040.1946677664840.3093152527560.0390593068180.1624745081610.0124061675029-0.02089571643660.2122113949770.0229319320370.16238929820548.72838815981.60692616039.24640283854
62.65694436378-1.854765425620.4069958284211.4574009784-0.4744690672890.2829683316830.368555245078-0.4664638134150.5510737115090.0510277209289-0.278561923366-0.475204169011-0.1672763938480.767892728563-0.09267304850380.341503731946-0.1084377129160.04460697402840.501855402529-0.09016171394980.35165996768849.372132035517.752570949816.5186280095
72.83763961639-0.437783401986-0.3555976829671.33580345910.7534148055233.226318026390.09083751543560.203438642376-0.0502227953789-0.054680136059-0.07369144543260.04577675993050.138575893609-0.0522246467141-0.04118277976280.1375647080480.0198838563594-0.01772733865640.1353779622630.01831557986720.13099155378641.285701320810.1107792206-3.0238541627
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 28 )2 - 281 - 27
22chain 'A' and (resid 29 through 47 )29 - 4728 - 46
33chain 'A' and (resid 48 through 164 )48 - 16447 - 163
44chain 'A' and (resid 165 through 189 )165 - 189164 - 188
55chain 'A' and (resid 190 through 299 )190 - 299189 - 298
66chain 'A' and (resid 300 through 317 )300 - 317299 - 316
77chain 'A' and (resid 318 through 347 )318 - 347317 - 346

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