[English] 日本語
Yorodumi- PDB-1q9j: Structure of polyketide synthase associated protein 5 from Mycoba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q9j | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of polyketide synthase associated protein 5 from Mycobacterium tuberculosis | ||||||
Components | Polyketide synthase associated protein 5 | ||||||
Keywords | LIGASE / POLYKETIDE SYNTHASE ASSOCIATED PROTEIN / CONJUGATING ENZYME PAPA5 / Mycobacterium tuberculosis / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information phenolphthiocerol/phthiocerol/phthiodiolone dimycocerosyl transferase / Dimycocersyl phthiocerol biosynthesis / O-acyltransferase activity / DIM/DIP cell wall layer assembly / lipid biosynthetic process / acyltransferase activity / acyltransferase activity, transferring groups other than amino-acyl groups / lipid metabolic process Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.75 Å | ||||||
Authors | Buglino, J. / Onwueme, K.C. / Quadri, L.E. / Lima, C.D. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Crystal Structure of PapA5, a Phthiocerol Dimycocerosyl Transferase from Mycobacterium tuberculosis Authors: Buglino, J. / Onwueme, K.C. / Ferreras, J.A. / Quadri, L.E. / Lima, C.D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1q9j.cif.gz | 163.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1q9j.ent.gz | 131.3 KB | Display | PDB format |
PDBx/mmJSON format | 1q9j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q9/1q9j ftp://data.pdbj.org/pub/pdb/validation_reports/q9/1q9j | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
2 |
| ||||||||||
3 |
| ||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 45465.531 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: PAPA5 / Plasmid: PSMT3 (MODIFIED PET28B) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P96208, UniProt: P9WIN5*PLUS #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 3.99 Å3/Da / Density % sol: 68.9 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 5-10% PEG 4000, 0.2M Ammonium Acetate, 5% Glycerol, 0.02M DTT, 0.1M Sodium Citrate pH 5, pH 5., VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| ||||||||||||||||||
Detector |
| ||||||||||||||||||
Radiation |
| ||||||||||||||||||
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.75→20 Å / Num. all: 35971 / Num. obs: 34892 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 70.1 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 12.6 | ||||||||||||||||||
Reflection shell | Resolution: 2.75→2.85 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 2 / Num. unique all: 3074 / % possible all: 86.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SIRAS / Resolution: 2.75→20 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.1484 Å2 / ksol: 0.304098 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.7 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error free: 0.51 Å / Luzzati sigma a free: 0.59 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→20 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.75→2.92 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|