+Open data
-Basic information
Entry | Database: PDB / ID: 1dcd | ||||||
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Title | DESULFOREDOXIN COMPLEXED WITH CD2+ | ||||||
Components | PROTEIN (DESULFOREDOXIN) | ||||||
Keywords | ELECTRON TRANSPORT / RUBREDOXIN TYPE PROTEIN | ||||||
Function / homology | Desulforedoxin / Desulfoferrodoxin, N-terminal domain / Desulfoferrodoxin, N-terminal domain superfamily / Desulfoferrodoxin, N-terminal domain / iron ion binding / : / Desulforedoxin Function and homology information | ||||||
Biological species | Desulfovibrio gigas (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Archer, M. / Carvalho, A.L. / Teixeira, S. / Romao, M.J. | ||||||
Citation | Journal: Protein Sci. / Year: 1999 Title: Structural studies by X-ray diffraction on metal substituted desulforedoxin, a rubredoxin-type protein. Authors: Archer, M. / Carvalho, A.L. / Teixeira, S. / Moura, I. / Moura, J.J. / Rusnak, F. / Romao, M.J. #1: Journal: J.Mol.Biol. / Year: 1995 Title: Crystal structure of desulforedoxin from Desulfovibrio gigas determined at 1.8 A resolution: a novel non-heme iron protein structure. Authors: Archer, M. / Huber, R. / Tavares, P. / Moura, I. / Moura, J.J. / Carrondo, M.A. / Sieker, L.C. / LeGall, J. / Romao, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dcd.cif.gz | 25.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dcd.ent.gz | 16.5 KB | Display | PDB format |
PDBx/mmJSON format | 1dcd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dcd_validation.pdf.gz | 371.6 KB | Display | wwPDB validaton report |
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Full document | 1dcd_full_validation.pdf.gz | 371 KB | Display | |
Data in XML | 1dcd_validation.xml.gz | 2.8 KB | Display | |
Data in CIF | 1dcd_validation.cif.gz | 4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/1dcd ftp://data.pdbj.org/pub/pdb/validation_reports/dc/1dcd | HTTPS FTP |
-Related structure data
Related structure data | 1cfwC 1dhgC 1dxgS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.939027, -0.226955, -0.258303), Vector: |
-Components
#1: Protein/peptide | Mass: 3807.350 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio gigas (bacteria) / Cellular location: CYTOPLASM / Cellular location (production host): CYTOPLASM / Gene (production host): DSR / Production host: Escherichia coli (E. coli) / References: UniProt: P00273 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5 Details: 30% ETHANOL, 0.1 M SODIUM ACETATE PH 5, 0.2 M CACL2, pH 5.0 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.6 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→14.8 Å / Num. all: 4403 / Num. obs: 4403 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rsym value: 0.115 / Net I/σ(I): 8 |
Reflection shell | Resolution: 1.98→2.05 Å / Mean I/σ(I) obs: 2.5 / Rsym value: 0.432 / % possible all: 96.4 |
Reflection | *PLUS Num. measured all: 28142 / Rmerge(I) obs: 0.115 |
Reflection shell | *PLUS % possible obs: 96.4 % / Rmerge(I) obs: 0.359 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DXG Resolution: 2→14.8 Å / Num. parameters: 2325 / Num. restraintsaints: 2656 / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: GEOMETRIC RESTRAINTS WERE APPLIED TO THE METAL CENTER (DFIX CD S 2.55 A)
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 2 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 576 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→14.8 Å
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Refine LS restraints |
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