[English] 日本語
Yorodumi- PDB-2wzt: Crystal structure of a mycobacterium aldo-keto reductase in its a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wzt | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a mycobacterium aldo-keto reductase in its apo and liganded form | ||||||
Components | ALDO-KETO REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information small molecule metabolic process / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM SMEGMATIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Scoble, J. / McAlister, A.D. / Fulton, Z. / Troy, S. / Byres, E. / Vivian, J.P. / Brammananth, R. / Wilce, M.C.J. / Le Nours, J. / Zaker-Tabrizi, L. ...Scoble, J. / McAlister, A.D. / Fulton, Z. / Troy, S. / Byres, E. / Vivian, J.P. / Brammananth, R. / Wilce, M.C.J. / Le Nours, J. / Zaker-Tabrizi, L. / Coppel, R.L. / Crellin, P.K. / Rossjohn, J. / Beddoe, T. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Crystal Structure and Comparative Functional Analyses of a Mycobacterium Aldo-Keto Reductase. Authors: Scoble, J. / Mcalister, A.D. / Fulton, Z. / Troy, S. / Byres, E. / Vivian, J.P. / Brammananth, R. / Wilce, M.C.J. / Le Nours, J. / Zaker-Tabrizi, L. / Coppel, R.L. / Crellin, P.K. / Rossjohn, J. / Beddoe, T. | ||||||
History |
| ||||||
Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2wzt.cif.gz | 120.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2wzt.ent.gz | 93.8 KB | Display | PDB format |
PDBx/mmJSON format | 2wzt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wzt_validation.pdf.gz | 431.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2wzt_full_validation.pdf.gz | 436.4 KB | Display | |
Data in XML | 2wzt_validation.xml.gz | 24.4 KB | Display | |
Data in CIF | 2wzt_validation.cif.gz | 36.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wz/2wzt ftp://data.pdbj.org/pub/pdb/validation_reports/wz/2wzt | HTTPS FTP |
-Related structure data
Related structure data | 2wzmC 1vbjS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 4 / Auth seq-ID: 11 - 268 / Label seq-ID: 11 - 268
NCS oper: (Code: given Matrix: (0.8724, -0.003268, 0.4889), Vector: |
-Components
#1: Protein | Mass: 29973.307 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM SMEGMATIS (bacteria) / Strain: MC2 155 / Plasmid: PDEST17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0QV09, EC: 1.1.1.218 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.1 % / Description: NONE |
---|---|
Crystal grow | pH: 5.1 / Details: 20% PEG 0.2M CACL2 0.1M NA CACODYLATE PH 5.1 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKE / Detector: IMAGE PLATE / Date: Oct 1, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→26.3 Å / Num. obs: 40896 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.3 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1VBJ Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 5.398 / SU ML: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.136 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.078 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|