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- PDB-1sau: The Gamma subunit of the dissimilatory sulfite reductase (DsrC) f... -

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Basic information

Entry
Database: PDB / ID: 1sau
TitleThe Gamma subunit of the dissimilatory sulfite reductase (DsrC) from Archaeoglobus fulgidus at 1.1 A resolution
Componentssulfite reductase, desulfoviridin-type subunit gamma
KeywordsOXIDOREDUCTASE / ORTHOGONAL HELICAL BUNDLE
Function / homology
Function and homology information


tRNA wobble position uridine thiolation / sulfur carrier activity / cytoplasm
Similarity search - Function
DsrC protein, C-terminal domain / Dissimilatory Siroheme-sulfite Reductase; Chain: A; domain 1 / DsrC protein, N-terminal domain / Sulphur transfer protein DsrC/TusE / DsrC-like domain superfamily / DsrC-like protein, C-terminal domain / DsrC-like protein, N-terminal domain / DsrC like protein / Arc Repressor Mutant, subunit A / 2-Layer Sandwich ...DsrC protein, C-terminal domain / Dissimilatory Siroheme-sulfite Reductase; Chain: A; domain 1 / DsrC protein, N-terminal domain / Sulphur transfer protein DsrC/TusE / DsrC-like domain superfamily / DsrC-like protein, C-terminal domain / DsrC-like protein, N-terminal domain / DsrC like protein / Arc Repressor Mutant, subunit A / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Sulfite reductase, desulfoviridin-type subunit gamma (DsvC)
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.12 Å
AuthorsMander, G.J. / Weiss, M.S. / Hedderich, R. / Kahnt, J. / Ermler, U. / Warkentin, E.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Determination of a novel structure by a combination of long-wavelength sulfur phasing and radiation-damage-induced phasing.
Authors: Weiss, M.S. / Mander, G. / Hedderich, R. / Diederichs, K. / Ermler, U. / Warkentin, E.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Determination of a novel structure by a combination of long-wavelength sulfur phasing and radiation-damage-induced phasing.
Authors: Weiss, M.S. / Mander, G. / Hedderich, R. / Diederichs, K. / Ermler, U. / Warkentin, E.
History
DepositionFeb 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: sulfite reductase, desulfoviridin-type subunit gamma


Theoretical massNumber of molelcules
Total (without water)13,4991
Polymers13,4991
Non-polymers00
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.935, 46.528, 57.154
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein sulfite reductase, desulfoviridin-type subunit gamma / DsrC / dissimilatory sulfite reductase


Mass: 13498.659 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: DsrC / Plasmid: pCR2.1-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / K12 / References: UniProt: O28055
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.8 Å3/Da / Density % sol: 31.23 %
Crystal growTemperature: 277 K / pH: 9.5
Details: TRIS, MPD, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 9.50
Crystal grow
*PLUS
pH: 9.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
158 %(v/v)MPD1reservoir
20.1 MTris-HCl1reservoirpH9.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 11, 2002 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.1→20 Å / Num. obs: 40859 / % possible obs: 93.1 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 9.4 Å2 / Rsym value: 0.083 / Net I/σ(I): 21
Reflection shellResolution: 1.1→1.18 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 5.5 / Rsym value: 0.165 / % possible all: 73
Reflection
*PLUS
Highest resolution: 1.12 Å / Lowest resolution: 99 Å / Num. obs: 40862 / Observed criterion σ(I): 0 / Redundancy: 5 % / Num. measured all: 205663 / Rmerge(I) obs: 0.093
Reflection shell
*PLUS
Highest resolution: 1.12 Å / Lowest resolution: 1.15 Å / % possible obs: 73.5 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 4.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
MLPHAREphasing
SHELXL-97refinement
RefinementMethod to determine structure: SAD / Resolution: 1.12→20 Å / Num. parameters: 10819 / Num. restraintsaints: 14685 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.044
RfactorNum. reflection% reflectionSelection details
Rfree0.137 1973 5.2 %RANDOM
all0.109 39635 --
obs0.109 -95 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228. riding hydrogens were used in refinement.
Refine analyzeNum. disordered residues: 18 / Occupancy sum hydrogen: 938 / Occupancy sum non hydrogen: 1062.5
Refinement stepCycle: LAST / Resolution: 1.12→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms941 0 0 149 1090
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.028
X-RAY DIFFRACTIONs_zero_chiral_vol0.096
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.091
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.036
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.048
X-RAY DIFFRACTIONs_approx_iso_adps0.09
LS refinement shellResolution: 1.12→1.17 Å /
Rfactor% reflection
Rwork0.136 -
obs-73 %
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor obs: 0.108 / Rfactor Rwork: 0.108
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 8.2 Å2
LS refinement shell
*PLUS
Lowest resolution: 1.15 Å

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