[English] 日本語
Yorodumi- PDB-1gu9: Crystal Structure of Mycobacterium tuberculosis Alkylperoxidase AhpD -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gu9 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Mycobacterium tuberculosis Alkylperoxidase AhpD | ||||||
Components | ALKYLHYDROPEROXIDASE D | ||||||
Keywords | OXIDOREDUCTASE / ALKYLHYDROPEROXIDASE / TUBERCULOSIS | ||||||
Function / homology | AhpD-like / AhpD-like / Up-down Bundle / Mainly Alpha Function and homology information | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | ||||||
Authors | Nunn, C.M. / Djordjevic, S. / Hillas, P.J. / Nishida, C. / Ortiz de Montellano, P.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: The Crystal Structure of Mycobacterium Tuberculosis Alkylhydroperoxidase Ahpd, a Potential Target for Antitubercular Drug Design Authors: Nunn, C.M. / Djordjevic, S. / Hillas, P.J. / Nishida, C. / Ortiz de Montellano, P.R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1gu9.cif.gz | 389.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1gu9.ent.gz | 334.5 KB | Display | PDB format |
PDBx/mmJSON format | 1gu9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gu9_validation.pdf.gz | 528.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1gu9_full_validation.pdf.gz | 608.5 KB | Display | |
Data in XML | 1gu9_validation.xml.gz | 87.3 KB | Display | |
Data in CIF | 1gu9_validation.cif.gz | 120.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gu/1gu9 ftp://data.pdbj.org/pub/pdb/validation_reports/gu/1gu9 | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18942.205 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) #2: Water | ChemComp-HOH / | Sequence details | RESIDUE 104 IN ALL CHAINS WAS FOUND TO BE A METHIONINE | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 6 Details: 100MM SODIUM CITRATE BUFFER, PH 5.6, CONTAINING 200MM AMMONIUM ACETATE AND 26% PEG 4000. MIXED IN EQUAL VOLUME WITH AHPD (4.5 MG/ML) IN 25 MM MOPS BUFFER, PH 7.2, CONTAINING 50 MM KCL, 10% GLYCEROL, 0.1MM EDTA | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.2 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 110 K | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.88550,0.918400,0.978900 , 0.97877 | |||||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 15, 2001 / Details: MIRRORS | |||||||||||||||
Radiation | Monochromator: SI 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
| |||||||||||||||
Reflection | Resolution: 1.9→30 Å / Num. obs: 136927 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 7.2 | |||||||||||||||
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.75 / % possible all: 99.3 | |||||||||||||||
Reflection | *PLUS Lowest resolution: 500 Å / Num. measured all: 1263412 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 99.3 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 1.9→29.6 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.9056 Å2 / ksol: 0.349187 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.8 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→29.6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.97 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 500 Å / Rfactor Rfree: 0.31 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 33.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|