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Yorodumi- PDB-7gep: SULFITE REDUCTASE HEMOPROTEIN IN COMPLEX WITH A PARTIALLY OXIDIZE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7gep | |||||||||
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Title | SULFITE REDUCTASE HEMOPROTEIN IN COMPLEX WITH A PARTIALLY OXIDIZED SULFIDE SPECIES | |||||||||
Components | SULFITE REDUCTASE HEMOPROTEIN | |||||||||
Keywords | OXIDOREDUCTASE / SIROHEME FEIII / [4FE-4S] +2 / SULFIDE COMPLEX / INTERMEDIATE | |||||||||
Function / homology | Function and homology information assimilatory sulfite reductase (NADPH) / sulfite reductase (NADPH) activity / sulfite reductase (ferredoxin) activity / sulfite reductase complex (NADPH) / sulfite reductase activity / sulfate assimilation / hydrogen sulfide biosynthetic process / cysteine biosynthetic process / NADP binding / 4 iron, 4 sulfur cluster binding ...assimilatory sulfite reductase (NADPH) / sulfite reductase (NADPH) activity / sulfite reductase (ferredoxin) activity / sulfite reductase complex (NADPH) / sulfite reductase activity / sulfate assimilation / hydrogen sulfide biosynthetic process / cysteine biosynthetic process / NADP binding / 4 iron, 4 sulfur cluster binding / heme binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Crane, B.R. / Getzoff, E.D. | |||||||||
Citation | Journal: Biochemistry / Year: 1997 Title: Probing the catalytic mechanism of sulfite reductase by X-ray crystallography: structures of the Escherichia coli hemoprotein in complex with substrates, inhibitors, intermediates, and products. Authors: Crane, B.R. / Siegel, L.M. / Getzoff, E.D. #1: Journal: Science / Year: 1995 Title: Sulfite Reductase Structure at 1.6 A: Evolution and Catalysis for Reduction of Inorganic Anions Authors: Crane, B.R. / Siegel, L.M. / Getzoff, E.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7gep.cif.gz | 119.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7gep.ent.gz | 88.8 KB | Display | PDB format |
PDBx/mmJSON format | 7gep.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7gep_validation.pdf.gz | 525.2 KB | Display | wwPDB validaton report |
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Full document | 7gep_full_validation.pdf.gz | 534.8 KB | Display | |
Data in XML | 7gep_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 7gep_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ge/7gep ftp://data.pdbj.org/pub/pdb/validation_reports/ge/7gep | HTTPS FTP |
-Related structure data
Related structure data | 2gepC 3geoC 4gepC 5gepC 6gepC 8gepC 1gep 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 55747.715 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: B Description: PBR322 DERIVATIVE CONTAINING ESCHERICHIA COLI CYSIJ AND S. TYPHIMURIUM CYSG UNDER CONTROL OF THE CYSJIH PROMOTOR EXPRESSED IN A S. TYPHIMURIUM CYSI AUXOTROPH Gene: CYSIJ / Plasmid: PJYW613 / Gene (production host): CYSIJ / Production host: Salmonella typhimurium (bacteria) / Strain (production host): CYSI68 References: UniProt: P17846, assimilatory sulfite reductase (NADPH) |
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-Non-polymers , 5 types, 352 molecules
#2: Chemical | ChemComp-NA / |
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#3: Chemical | ChemComp-SF4 / |
#4: Chemical | ChemComp-SRM / |
#5: Chemical | ChemComp-SX / |
#6: Water | ChemComp-HOH / |
-Details
Nonpolymer details | THE PUTATIVE S-O SPECIES IS BOUND TO THE SIROHEME IRON THROUGH SULFUR. OXIDIZED, SIROHEME FEIII ...THE PUTATIVE S-O SPECIES IS BOUND TO THE SIROHEME IRON THROUGH SULFUR. OXIDIZED, SIROHEME FEIII [4FE-4S] +2, COMPLEX WITH PARTIALLY OXIDIZED SULFIDE (PUTATIVE S-O SPECIES). THIS IS NAMED HP-S IN THE PRIMARY REFERENCE. |
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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: 2.13 Å3/Da / Density % sol: 40 % / Description: CRYSTALS ARE ISOMORPHOUS WITH 1GEP | |||||||||||||||||||||||||
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Crystal grow | pH: 7.7 / Details: pH 7.7 | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 1.08 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Jun 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 18253 / % possible obs: 92.1 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rsym value: 0.096 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.4→2.5 Å / Mean I/σ(I) obs: 3.6 / Rsym value: 0.274 / % possible all: 70.5 |
Reflection | *PLUS Rmerge(I) obs: 0.096 |
Reflection shell | *PLUS % possible obs: 73.2 % / Rmerge(I) obs: 0.274 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GEP 1gep Resolution: 2.4→10 Å / σ(F): 2
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Displacement parameters | Biso mean: 26.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 4 Å / Luzzati sigma a obs: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.5 Å
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.308 |