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- PDB-5fez: HydE from T. maritima in complex with (2R,4R)-MeSeTDA, 5'-deoxyad... -

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Basic information

Entry
Database: PDB / ID: 5fez
TitleHydE from T. maritima in complex with (2R,4R)-MeSeTDA, 5'-deoxyadenosine and methionine
Components[FeFe] hydrogenase maturase subunit HydE
KeywordsOXIDOREDUCTASE / Radical SAM enzyme / complex / FeFe-hydrogenase maturase / thiazolidine
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
[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 class I ...[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 class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
5'-DEOXYADENOSINE / Chem-9SE / METHIONINE / Fe4-Se4 cluster / [FeFe] hydrogenase maturase subunit HydE
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsRohac, R. / Amara, P. / Benjdia, A. / Martin, L. / Ruffie, P. / Favier, A. / Berteau, O. / Mouesca, J.M. / Fontecilla-Camps, J.C. / Nicolet, Y.
CitationJournal: Nat.Chem. / Year: 2016
Title: Carbon-sulfur bond-forming reaction catalysed by the radical SAM enzyme HydE.
Authors: Rohac, R. / Amara, P. / Benjdia, A. / Martin, L. / Ruffie, P. / Favier, A. / Berteau, O. / Mouesca, J.M. / Fontecilla-Camps, J.C. / Nicolet, Y.
History
DepositionDec 17, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)45,29711
Polymers41,0091
Non-polymers4,28810
Water9,044502
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-4 kcal/mol
Surface area14620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.800, 78.870, 86.250
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: 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 (E. coli)
References: UniProt: Q9X0Z6, Oxidoreductases; Acting on a sulfur group of donors

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Non-polymers , 7 types, 512 molecules

#2: Chemical ChemComp-SFS / Fe4-Se4 cluster


Mass: 539.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4Se4
#3: 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
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-5AD / 5'-DEOXYADENOSINE


Mass: 251.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O3
#6: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#7: Chemical ChemComp-9SE / (2~{R},4~{R})-2-methyl-1,3-selenazolidine-2,4-dicarboxylic acid


Mass: 238.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H9NO4Se
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG4000, Lithium sulfate, CHAPS, TrisHCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.35→44 Å / Num. obs: 76623 / % possible obs: 99.8 % / Redundancy: 5.9 % / Net I/σ(I): 15.27
Reflection shellResolution: 1.35→1.43 Å / Rsym value: 0.939

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IIX

3iix


Resolution: 1.35→38.27 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.796 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13519 3833 5 %RANDOM
Rwork0.11904 ---
obs0.11982 72790 99.87 %-
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: 17.191 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20 Å20 Å2
2---0.13 Å20 Å2
3----1.16 Å2
Refinement stepCycle: 1 / Resolution: 1.35→38.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2741 0 215 502 3458
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.023233
X-RAY DIFFRACTIONr_bond_other_d0.0030.023164
X-RAY DIFFRACTIONr_angle_refined_deg2.2772.0944465
X-RAY DIFFRACTIONr_angle_other_deg1.43437340
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9465386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.42523.435131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.88715546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3931527
X-RAY DIFFRACTIONr_chiral_restr0.2270.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213441
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02673
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_it1.6731.3561469
X-RAY DIFFRACTIONr_mcbond_other1.6731.3561468
X-RAY DIFFRACTIONr_mcangle_it1.8112.0381859
X-RAY DIFFRACTIONr_mcangle_other1.8112.0381860
X-RAY DIFFRACTIONr_scbond_it3.1351.6431764
X-RAY DIFFRACTIONr_scbond_other3.1351.6421762
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4942.3752587
X-RAY DIFFRACTIONr_long_range_B_refined3.75814.86214707
X-RAY DIFFRACTIONr_long_range_B_other3.75814.86214708
X-RAY DIFFRACTIONr_rigid_bond_restr9.21436393
X-RAY DIFFRACTIONr_sphericity_free32.399539
X-RAY DIFFRACTIONr_sphericity_bonded9.39256759
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 278 -
Rwork0.248 5284 -
obs--99.07 %

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