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- PDB-8qmn: [FeFe]-hydrogenase maturase HydE from T. maritima - dialysis expe... -

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Basic information

Entry
Database: PDB / ID: 8qmn
Title[FeFe]-hydrogenase maturase HydE from T. maritima - dialysis experiment - empty structure
Components[FeFe] hydrogenase maturase subunit HydE
KeywordsMETAL BINDING PROTEIN / [FeFe]-hydrogenase / radical SAM protein / H-cluster / Complex-B / iron-sulfur 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
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: 1.48 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 23, 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)42,4848
Polymers40,9911
Non-polymers1,4937
Water8,683482
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-65 kcal/mol
Surface area15300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.740, 83.630, 70.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 40991.348 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 , 5 types, 489 molecules

#2: Chemical ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS / CHAPS detergent


Mass: 614.877 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#3: 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
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 482 / 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: 2.29 Å3/Da / Density % sol: 46.34 %
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: Apr 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.48→54 Å / Num. obs: 62674 / % possible obs: 98.5 % / Redundancy: 6.4 % / CC1/2: 0.999 / Net I/σ(I): 13.12
Reflection shellResolution: 1.48→1.52 Å / Num. unique obs: 8039 / CC1/2: 0.257

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→53.91 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.974 / SU B: 3.754 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17695 3131 5 %RANDOM
Rwork0.13309 ---
obs0.13528 59575 98.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.466 Å2
Baniso -1Baniso -2Baniso -3
1--1.83 Å20 Å2-0 Å2
2--2.26 Å2-0 Å2
3----0.42 Å2
Refinement stepCycle: 1 / Resolution: 1.48→53.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2846 0 61 482 3389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0123298
X-RAY DIFFRACTIONr_bond_other_d0.0030.0163210
X-RAY DIFFRACTIONr_angle_refined_deg1.8121.6824534
X-RAY DIFFRACTIONr_angle_other_deg0.6971.5867468
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9615432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.886533
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.7210609
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.120.2504
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023860
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02762
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3162.1341518
X-RAY DIFFRACTIONr_mcbond_other1.3152.1341517
X-RAY DIFFRACTIONr_mcangle_it1.7893.8381913
X-RAY DIFFRACTIONr_mcangle_other1.7893.8381914
X-RAY DIFFRACTIONr_scbond_it1.6232.4791780
X-RAY DIFFRACTIONr_scbond_other1.6192.4791767
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2444.4372557
X-RAY DIFFRACTIONr_long_range_B_refined4.67626.314023
X-RAY DIFFRACTIONr_long_range_B_other3.89823.813867
X-RAY DIFFRACTIONr_rigid_bond_restr3.29936508
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.48→1.518 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 194 -
Rwork0.342 3997 -
obs--90.64 %

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