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- PDB-5few: HydE from T. maritima in complex with S-adenosyl-L-cysteine (fina... -

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Basic information

Entry
Database: PDB / ID: 5few
TitleHydE from T. maritima in complex with S-adenosyl-L-cysteine (final product)
Components[FeFe] hydrogenase maturase subunit HydE
KeywordsOXIDOREDUCTASE / Radical SAM enzyme / complex / FeFe-hydrogenase maturase / thazolidine
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 ...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 class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-41K / S-adenosyl-L-cysteine / METHIONINE / 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: 1.17 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id

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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)45,60213
Polymers41,0091
Non-polymers4,59212
Water7,638424
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-42 kcal/mol
Surface area14700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.990, 78.970, 86.270
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 , 8 types, 436 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-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.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#6: 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
#7: 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
#8: 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
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.12 Å3/Da / Density % sol: 41.92 %
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: Jul 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.17→44 Å / Num. obs: 118444 / % possible obs: 99.6 % / Redundancy: 20 % / Net I/σ(I): 19.08
Reflection shellResolution: 1.17→1.24 Å / Rsym value: 1.744

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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: 1.17→43.9 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.964 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13233 5529 4.7 %RANDOM
Rwork0.10974 ---
obs0.11083 112915 99.7 %-
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: 17.305 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20 Å20 Å2
2--0.1 Å20 Å2
3----0.93 Å2
Refinement stepCycle: 1 / Resolution: 1.17→43.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2745 0 249 424 3418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0193313
X-RAY DIFFRACTIONr_bond_other_d0.0030.023239
X-RAY DIFFRACTIONr_angle_refined_deg2.4892.0854583
X-RAY DIFFRACTIONr_angle_other_deg1.2693.0037529
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9165397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.30423.504137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.13315562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.081528
X-RAY DIFFRACTIONr_chiral_restr0.2080.2541
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213523
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02686
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_it1.6491.3821491
X-RAY DIFFRACTIONr_mcbond_other1.6491.3831490
X-RAY DIFFRACTIONr_mcangle_it1.8842.0821888
X-RAY DIFFRACTIONr_mcangle_other1.8832.0811889
X-RAY DIFFRACTIONr_scbond_it2.9461.7041822
X-RAY DIFFRACTIONr_scbond_other2.9471.7041821
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3372.4552671
X-RAY DIFFRACTIONr_long_range_B_refined3.49914.914648
X-RAY DIFFRACTIONr_long_range_B_other3.49914.914649
X-RAY DIFFRACTIONr_rigid_bond_restr6.0636548
X-RAY DIFFRACTIONr_sphericity_free31.438545
X-RAY DIFFRACTIONr_sphericity_bonded9.95156821
LS refinement shellResolution: 1.167→1.197 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 310 -
Rwork0.24 8142 -
obs--97.4 %

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