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Basic information

Entry
Database: PDB / ID: 4jxc
TitleX-ray snapshots of possible intermediates in the time course of synthesis and degradation of protein-bound Fe4S4 clusters
ComponentsFEFE-HYDROGENASE MATURASE
KeywordsOXIDOREDUCTASE / Radical SAM Protein / FeFe-hydrogenase active site Assembly / Fe4S4 cluster / S-adenosyl-L-methionine
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
FE2/S2 (INORGANIC) CLUSTER / HYDROSULFURIC ACID / ISOPROPYL ALCOHOL / S-ADENOSYLMETHIONINE / IRON/SULFUR CLUSTER / [FeFe] hydrogenase maturase subunit HydE
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsNicolet, Y. / Rohac, R. / Martin, L. / Fontecilla-Camps, J.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: X-ray snapshots of possible intermediates in the time course of synthesis and degradation of protein-bound Fe4S4 clusters.
Authors: Nicolet, Y. / Rohac, R. / Martin, L. / Fontecilla-Camps, J.C.
History
DepositionMar 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FEFE-HYDROGENASE MATURASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,34616
Polymers39,8731
Non-polymers4,47315
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.132, 78.729, 86.209
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 / Radical SAM domain protein


Mass: 39873.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_1269, ThemaDRAFT_0043 / Plasmid: pHydE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9X0Z6

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Non-polymers , 10 types, 343 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-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical
ChemComp-1N7 / CHAPSO / 2-hydroxy-N,N-dimethyl-3-sulfo-N-(3-{[(3beta,5beta,7beta,12beta)-3,7,12-trihydroxy-24-oxocholan-24-yl]amino}propyl)propan-1-aminium


Mass: 631.884 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C32H59N2O8S / Comment: detergent*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#7: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2S
#8: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#10: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O

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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: 2.18 Å3/Da / Density % sol: 43.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM Tris, 200 mM Li2SO4, 30% PEG 4000, Anaerobic chamber (N2/H2 95/5%) , pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 21, 2005
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.45→60 Å / Num. all: 119182 / Num. obs: 101819 / % possible obs: 85.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.45→1.54 Å / % possible all: 88.06

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0070refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CIW

3ciw


Resolution: 1.5→58.12 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.316 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16553 2809 5.1 %RANDOM
Rwork0.1214 ---
all0.12363 52356 --
obs0.12363 52356 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.767 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å20 Å2
2---0.09 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.5→58.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2726 0 206 328 3260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223147
X-RAY DIFFRACTIONr_bond_other_d0.0020.022234
X-RAY DIFFRACTIONr_angle_refined_deg1.742.0784329
X-RAY DIFFRACTIONr_angle_other_deg1.0135494
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.8315.053377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.57623.413126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.72215540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3411525
X-RAY DIFFRACTIONr_chiral_restr0.1120.2519
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213234
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02584
X-RAY DIFFRACTIONr_mcbond_it2.35721788
X-RAY DIFFRACTIONr_mcbond_other1.1972720
X-RAY DIFFRACTIONr_mcangle_it3.10732913
X-RAY DIFFRACTIONr_scbond_it2.95621359
X-RAY DIFFRACTIONr_scangle_it4.02831390
X-RAY DIFFRACTIONr_rigid_bond_restr1.82635376
X-RAY DIFFRACTIONr_sphericity_free10.0433332
X-RAY DIFFRACTIONr_sphericity_bonded3.84735286
LS refinement shellResolution: 1.502→1.541 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 178 -
Rwork0.16 3283 -
obs--83.74 %

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