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- PDB-1ucr: Three-dimensional crystal structure of dissimilatory sulfite redu... -

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Basic information

Entry
Database: PDB / ID: 1ucr
TitleThree-dimensional crystal structure of dissimilatory sulfite reductase D (DsrD)
ComponentsProtein dsvD
KeywordsUNKNOWN FUNCTION / dissimilatory sulfite reductase D / DNA binding motif / sulfate-reducing bacteria / winged-helix motif
Function / homologyDissimilatory sulphite reductase D / Dissimilatory sulfite reductase D (DsrD) / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha / Protein DsvD
Function and homology information
Biological speciesDesulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.2 Å
AuthorsMizuno, N. / Voordouw, G. / Miki, K. / Sarai, A. / Higuchi, Y.
CitationJournal: STRUCTURE / Year: 2003
Title: Crystal Structure of Dissimilatory Sulfite Reductase D (DsrD) Protein-Possible Interaction with B- and Z-DNA by Its Winged-Helix Motif
Authors: Mizuno, N. / Voordouw, G. / Miki, K. / Sarai, A. / Higuchi, Y.
History
DepositionApr 18, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein dsvD
B: Protein dsvD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1647
Polymers17,6842
Non-polymers4805
Water4,161231
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.025, 64.559, 45.218
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 Protein dsvD / dissimilatory sulfite reductase D / DsrD


Mass: 8841.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q46582
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.26 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: 73-75% saturated ammonium sulfate, pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Mizuno, N., (2000) Acta Crystallogr., D56, 754.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140-60 mg/mlprotein1drop
2100 %satammonium sulfate1drop
373-75 %satammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.708 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 2, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.708 Å / Relative weight: 1
ReflectionResolution: 1.2→100 Å / Num. obs: 55639
Reflection
*PLUS
Highest resolution: 1.2 Å / % possible obs: 99.8 % / Num. measured all: 565339 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
Highest resolution: 1.2 Å / Lowest resolution: 1.26 Å / % possible obs: 99.8 % / Num. unique obs: 8364 / Num. measured obs: 82965 / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
SHELXmodel building
SHELXL-97refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MLPHAREphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.2→10 Å / Num. parameters: 13068 / Num. restraintsaints: 15368 / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1803 5629 -RANDOM
Rwork0.1359 ---
all0.1411 55430 --
obs0.1381 51032 89.7 %-
Refine analyzeNum. disordered residues: 6 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1451
Refinement stepCycle: LAST / Resolution: 1.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1194 0 25 231 1450
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.035
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0284
X-RAY DIFFRACTIONs_zero_chiral_vol0.071
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.1
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.06
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.073
X-RAY DIFFRACTIONs_approx_iso_adps0.106
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / Rfactor Rwork: 0.1389
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.028
X-RAY DIFFRACTIONs_chiral_restr0.071
LS refinement shell
*PLUS
Highest resolution: 1.2 Å / Lowest resolution: 1.24 Å / Rfactor Rwork: 0.166 / Num. reflection obs: 5001

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