[English] 日本語
![](img/lk-miru.gif)
- PDB-5gep: SULFITE REDUCTASE HEMOPROTEIN CARBON MONOXIDE COMPLEX REDUCED WIT... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5gep | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | SULFITE REDUCTASE HEMOPROTEIN CARBON MONOXIDE COMPLEX REDUCED WITH CRII EDTA | |||||||||
![]() | SULFITE REDUCTASE HEMOPROTEIN | |||||||||
![]() | OXIDOREDUCTASE / SIROHEME FEII / [4FE-4S] +1 / CARBON MONOXIDE COMPLEX / INHIBITOR | |||||||||
Function / homology | ![]() 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 | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Crane, B.R. / Getzoff, E.D. | |||||||||
![]() | ![]() 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: ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 117 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 86.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 524.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 536.5 KB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 21 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2gepC ![]() 3geoC ![]() 4gepC ![]() 6gepC ![]() 7gepC ![]() 8gepC ![]() 1aopS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
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.) ![]() ![]() 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: ![]() References: UniProt: P17846, assimilatory sulfite reductase (NADPH) |
---|
-Non-polymers , 5 types, 366 molecules ![](data/chem/img/K.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/SRM.gif)
![](data/chem/img/CMO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/SRM.gif)
![](data/chem/img/CMO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-K / |
---|---|
#3: Chemical | ChemComp-SF4 / |
#4: Chemical | ChemComp-SRM / |
#5: Chemical | ChemComp-CMO / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 40 % Description: CRYSTALS ARE ISOMORPHOUS WITH THOSE FOR 1AOP. DATA REDUCTION STATISTICS ARE REPORTED FOR CRYSTALS CONTAINING BOTH PHOSPHATE AND CARBON MONOXIDE BOUND TO THE SIROHEME IRON, EACH IN ...Description: CRYSTALS ARE ISOMORPHOUS WITH THOSE FOR 1AOP. DATA REDUCTION STATISTICS ARE REPORTED FOR CRYSTALS CONTAINING BOTH PHOSPHATE AND CARBON MONOXIDE BOUND TO THE SIROHEME IRON, EACH IN PARTIAL OCCUPANCY. REFINEMENT STATISTICS ARE GIVEN FOR A MODEL REFINED AGAINST DIFFRACTION DATA EXTRAPOLATED TO REPRESENT CO BOUND IN FULL OCCUPANCY. SEE PRIMARY REFERENCE FOR DETAILS. | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.7 Details: pH 7.7 OXIDIZED CRYSTALS WERE REDUCED WITH CRII EDTA IN THE PRESENCE OF CO. SIROHEME HAS FEII AND THE [4FE-4S] CLUSTER IS +1. CARBON MONOXIDE IS BOUND TO THE SIROHEME IRON THROUGH CARBON. ...Details: pH 7.7 OXIDIZED CRYSTALS WERE REDUCED WITH CRII EDTA IN THE PRESENCE OF CO. SIROHEME HAS FEII AND THE [4FE-4S] CLUSTER IS +1. CARBON MONOXIDE IS BOUND TO THE SIROHEME IRON THROUGH CARBON. THIS IS NAMED HP-CO IN THE PRIMARY REFERENCE. | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 277 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 11, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40 Å / Num. obs: 26602 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rsym value: 0.095 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.1→2.18 Å / Mean I/σ(I) obs: 3.7 / Rsym value: 0.286 / % possible all: 96.4 |
Reflection | *PLUS Rmerge(I) obs: 0.095 |
Reflection shell | *PLUS % possible obs: 96.4 % / Rmerge(I) obs: 0.286 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1AOP Resolution: 2.1→10 Å / σ(F): 2 Details: THE MODEL WAS REFINED AGAINST A DATA SET EXTRAPOLATED FROM DATA FOR A PARTIALLY OCCUPIED CO COMPLEX AND DATA FOR ENTRY 2AOP. SEE PRIMARY REFERENCE.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.8 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 4.5 Å / Luzzati sigma a obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.18 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.246 |