[English] 日本語
Yorodumi- PDB-2obc: The crystal structure of RibD from Escherichia coli in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2obc | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | The crystal structure of RibD from Escherichia coli in complex with a substrate analogue, ribose 5-phosphate (beta form), bound to the active site of the reductase domain | |||||||||
Components | Riboflavin biosynthesis protein ribD | |||||||||
Keywords | HYDROLASE / OXIDOREDUCTASE / alpha and beta class of proteins with mainly parallell strands / Substrate analogue complex (ribose 5-phosphate / beta-form) / Structural Genomics / HTP Escherichia coli proteins / Structural Proteomics in Europe / SPINE | |||||||||
Function / homology | Function and homology information 5-amino-6-(5-phosphoribosylamino)uracil reductase / diaminohydroxyphosphoribosylaminopyrimidine deaminase / diaminohydroxyphosphoribosylaminopyrimidine deaminase activity / 5-amino-6-(5-phosphoribosylamino)uracil reductase activity / riboflavin biosynthetic process / NADP binding / zinc ion binding Similarity search - Function | |||||||||
Biological species | Escherichia coli K12 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Moche, M. / Stenmark, P. / Gurmu, D. / Nordlund, P. / Structural Proteomics in Europe (SPINE) | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: The crystal structure of the bifunctional deaminase/reductase RibD of the riboflavin biosynthetic pathway in Escherichia coli: implications for the reductive mechanism. Authors: Stenmark, P. / Moche, M. / Gurmu, D. / Nordlund, P. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2obc.cif.gz | 151.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2obc.ent.gz | 118.4 KB | Display | PDB format |
PDBx/mmJSON format | 2obc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2obc_validation.pdf.gz | 467.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2obc_full_validation.pdf.gz | 488.7 KB | Display | |
Data in XML | 2obc_validation.xml.gz | 28.6 KB | Display | |
Data in CIF | 2obc_validation.cif.gz | 39.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ob/2obc ftp://data.pdbj.org/pub/pdb/validation_reports/ob/2obc | HTTPS FTP |
-Related structure data
Related structure data | 2g6vSC 2o7pC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
| ||||||||
Details | The content of the asymmetric unit (dimer) is the biological unit. |
-Components
#1: Protein | Mass: 44799.488 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: ribD / Plasmid: PT73.3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P25539, diaminohydroxyphosphoribosylaminopyrimidine deaminase, 5-amino-6-(5-phosphoribosylamino)uracil reductase #2: Sugar | ChemComp-RP5 / | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.7 Å3/Da / Density % sol: 66.76 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M MES pH 6.5, 3% (v/v) 1,6 Hexandiol, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 17, 2004 |
Radiation | Monochromator: DIAMOND (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 3→30 Å / Num. all: 26730 / Num. obs: 26665 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 59 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 3→3.1 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2435 / Rsym value: 0.409 / % possible all: 99.1 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2G6V Resolution: 3→28.86 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.877 / SU B: 37.269 / SU ML: 0.325 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.895 / ESU R Free: 0.393 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.742 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→28.86 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3→3.077 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|