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- PDB-4wcx: Crystal structure of HydG: A maturase of the [FeFe]-hydrogenase -

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Basic information

Entry
Database: PDB / ID: 4wcx
TitleCrystal structure of HydG: A maturase of the [FeFe]-hydrogenase
ComponentsBiotin and thiamin synthesis associated
KeywordsLYASE / [FeFe]-hydrogenase / maturase
Function / homology
Function and homology information


catalytic activity / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
[FeFe]-hydrogenase maturation HydG, radical SAM / ThiH/NocL/HydG-like / Biotin and Thiamin Synthesis associated domain / 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 / Aldolase-type TIM barrel
Similarity search - Domain/homology
ALANINE / : / HYDROSULFURIC ACID / METHIONINE / S-ADENOSYLMETHIONINE / IRON/SULFUR CLUSTER / Biotin and thiamin synthesis associated
Similarity search - Component
Biological speciesThermoanaerobacter italicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.59 Å
AuthorsDinis, P.C. / Harmer, J.E. / Driesener, R.C. / Roach, P.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: X-ray crystallographic and EPR spectroscopic analysis of HydG, a maturase in [FeFe]-hydrogenase H-cluster assembly.
Authors: Dinis, P. / Suess, D.L. / Fox, S.J. / Harmer, J.E. / Driesener, R.C. / De La Paz, L. / Swartz, J.R. / Essex, J.W. / Britt, R.D. / Roach, P.L.
History
DepositionSep 5, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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_asym_id / _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_asym_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_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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_asym_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.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Biotin and thiamin synthesis associated
C: Biotin and thiamin synthesis associated
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,68315
Polymers110,4462
Non-polymers2,23613
Water14,664814
1
A: Biotin and thiamin synthesis associated
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2788
Polymers55,2231
Non-polymers1,0557
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Biotin and thiamin synthesis associated
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4057
Polymers55,2231
Non-polymers1,1826
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.130, 56.190, 84.920
Angle α, β, γ (deg.)89.59, 83.62, 66.84
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AC

#1: Protein Biotin and thiamin synthesis associated


Mass: 55223.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter italicus (bacteria) / Strain: DSM 9252 / Ab9 / Gene: Thit_0582 / Plasmid: pRD003 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D3T7F1

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Non-polymers , 8 types, 827 molecules

#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-MET / METHIONINE / Methionine


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#4: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-ALA / ALANINE / Alanine


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#6: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE / Hydrogen sulfide


Mass: 34.081 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2S
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 814 / 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: 2.18 Å3/Da / Density meas: 43.7 Mg/m3 / Density % sol: 42.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM Bis-TRIS propane, 200 mM sodium fluoride, 20% polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763, 1.7389
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97631
21.73891
ReflectionResolution: 1.59→84.33 Å / Num. obs: 118163 / % possible obs: 96.2 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 12.3
Reflection shellResolution: 1.59→1.63 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 2.2 / % possible all: 94.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.59→84.327 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2134 1995 1.69 %Random Selection
Rwork0.1799 ---
obs0.1805 118154 96.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.59→84.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7179 0 80 814 8073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0167446
X-RAY DIFFRACTIONf_angle_d1.86610053
X-RAY DIFFRACTIONf_dihedral_angle_d14.5482786
X-RAY DIFFRACTIONf_chiral_restr0.0561104
X-RAY DIFFRACTIONf_plane_restr0.0071285
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.62980.34641360.30118136X-RAY DIFFRACTION94
1.6298-1.67380.29261490.26738197X-RAY DIFFRACTION95
1.6738-1.72310.27341450.23828144X-RAY DIFFRACTION95
1.7231-1.77870.23921160.22568249X-RAY DIFFRACTION95
1.7787-1.84230.25951530.21278248X-RAY DIFFRACTION96
1.8423-1.91610.26281530.21388311X-RAY DIFFRACTION96
1.9161-2.00330.23621220.20278334X-RAY DIFFRACTION96
2.0033-2.10890.22311520.20148240X-RAY DIFFRACTION96
2.1089-2.2410.22971470.19648374X-RAY DIFFRACTION97
2.241-2.41410.21381430.18868333X-RAY DIFFRACTION97
2.4141-2.6570.23631480.18738395X-RAY DIFFRACTION97
2.657-3.04150.23641460.18468447X-RAY DIFFRACTION98
3.0415-3.8320.1821400.15898392X-RAY DIFFRACTION97
3.832-84.44530.16881450.14218359X-RAY DIFFRACTION97

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