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Yorodumi- PDB-1h21: A novel iron centre in the split-Soret cytochrome c from Desulfov... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h21 | |||||||||
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Title | A novel iron centre in the split-Soret cytochrome c from Desulfovibrio desulfuricans ATCC 27774 | |||||||||
Components | SPLIT-SORET CYTOCHROME C | |||||||||
Keywords | CYTOCHROME / DIMERIC DI-HEME CYTOCHROME / STACKED HEME ARRANGEMENT / NOVEL FOLD / NOVEL IRON-SULFUR CENTRE / ELECTRON TRANSPORT / SULFATE RESPIRATION | |||||||||
Function / homology | Function and homology information anaerobic respiration / 2 iron, 2 sulfur cluster binding / metal ion binding Similarity search - Function | |||||||||
Biological species | DESULFOVIBRIO DESULFURICANS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å | |||||||||
Authors | Abreu, I.A. / Lourenco, A.I. / Xavier, A.V. / Legall, J. / Coelho, A.V. / Matias, P.M. / Pinto, D.M. / Carrondo, M.A. / Teixeira, M. / Saraiva, L.M. | |||||||||
Citation | Journal: J.Biol.Inorg.Chem. / Year: 2003 Title: A Novel Iron Centre in the Split-Soret Cytochrome C from Desulfovibrio Desulfuricans Atcc 27774 Authors: Abreu, I.A. / Lourenco, A.I. / Xavier, A.V. / Legall, J. / Coelho, A.V. / Matias, P.M. / Pinto, D.M. / Armenia Carrondo, M. / Teixeira, M. / Saraiva, L.M. #1: Journal: J.Biol.Inorg.Chem. / Year: 1997 Title: A Preliminary Analysis of the Three Dimensional Structure of Dimeric Di-Haem Split-Soret Cytochrome C from Desulfovibrio Desulfuricans Atcc 27774 at 2.5 A Resolution Using the MAD Phasing ...Title: A Preliminary Analysis of the Three Dimensional Structure of Dimeric Di-Haem Split-Soret Cytochrome C from Desulfovibrio Desulfuricans Atcc 27774 at 2.5 A Resolution Using the MAD Phasing Method: A Novel Cytochrome Fold with a Stacked Haem Arrangement Authors: Matias, P.M. / Morais, J. / Coelho, A.V. / Meijers, R. / Gonzalez, A. / Thompson, A.W. / Sieker, L. / Legall, J. / Carrondo, M.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h21.cif.gz | 197.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h21.ent.gz | 169.3 KB | Display | PDB format |
PDBx/mmJSON format | 1h21.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1h21_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 1h21_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 1h21_validation.xml.gz | 39.5 KB | Display | |
Data in CIF | 1h21_validation.cif.gz | 52.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/1h21 ftp://data.pdbj.org/pub/pdb/validation_reports/h2/1h21 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 26939.469 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO DESULFURICANS (bacteria) / References: UniProt: P81040 #2: Chemical | ChemComp-HEC / #3: Water | ChemComp-HOH / | Sequence details | GENBANK ENTRY AF465622 IS ON HOLD PENDING MANUSCRIPT ACCEPTANCE FOR PUBLICATION. SEQADV RECORDS ...GENBANK ENTRY AF465622 IS ON HOLD PENDING MANUSCRIPT | |
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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: 2.59 Å3/Da / Density % sol: 53 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5 Details: PROTEIN WAS CRYSTALLIZED FROM A SOLUTION CONTAINING 0.1-0.2 % (W/V) AGAROSE IN 12-15 % PEG 8K, 0.1M SODIUM ACETATE BUFFER PH 5.0 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop / Details: Matias, P.M., (1997) J.Biol.Inorg.Chem., 2, 507. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.7401 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1996 / Details: MIRRORS |
Radiation | Monochromator: SI (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.7401 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 34228 / % possible obs: 93 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.5→2.56 Å / Rmerge(I) obs: 0.074 / Mean I/σ(I) obs: 9.7 / % possible all: 86 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.5→20 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: FIRST 7 RESIDUES NOT VISIBLE IN ELECTRON DENSITY.
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Displacement parameters | Biso mean: 35.04 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 10 Å / Luzzati sigma a obs: 0.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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Xplor file |
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Refine LS restraints | *PLUS
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