+Open data
-Basic information
Entry | Database: PDB / ID: 3ne9 | ||||||
---|---|---|---|---|---|---|---|
Title | Chronobacterium ammoiniagenes apo-ACPS structure | ||||||
Components | Phosphopantetheine protein transferase, Ppt1p | ||||||
Keywords | TRANSFERASE / acyl carrier protein synthase / acyl carrier protein / fatty acid synthase / ACPS / Mycobacterium Tuberculosis Structural Proteomics Project / XMTB / Structural Genomics | ||||||
Function / homology | Function and homology information holo-[acyl-carrier-protein] synthase / holo-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Corynebacterium ammoniagenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å | ||||||
Authors | Gokulan, K. / Mycobacterium Tuberculosis Structural Proteomics Project (XMTB) | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2011 Title: Mycobacterium tuberculosis acyl carrier protein synthase adopts two different pH-dependent structural conformations. Authors: Gokulan, K. / Aggarwal, A. / Shipman, L. / Besra, G.S. / Sacchettini, J.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3ne9.cif.gz | 88.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3ne9.ent.gz | 73.8 KB | Display | PDB format |
PDBx/mmJSON format | 3ne9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ne9_validation.pdf.gz | 464.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3ne9_full_validation.pdf.gz | 484.1 KB | Display | |
Data in XML | 3ne9_validation.xml.gz | 20 KB | Display | |
Data in CIF | 3ne9_validation.cif.gz | 26.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ne/3ne9 ftp://data.pdbj.org/pub/pdb/validation_reports/ne/3ne9 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 16956.828 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium ammoniagenes (bacteria) Gene: ACPS, PPT1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: O31302 #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Sequence details | ACCORDING TO THE AUTHORS THE DISCREPANC | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.46 % |
---|---|
Crystal grow | Method: evaporation / pH: 6.5 Details: 100 mM MES buffer pH 6.5, 0.2 M ammonium sulfate, 30% PEG MME 5K, EVAPORATION |
-Data collection
Diffraction | Mean temperature: 120 K | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.9792, 0.97906, 0.96380 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 10, 1999 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
| ||||||||||||
Reflection | Resolution: 2.48→30 Å / Num. all: 16681 / Num. obs: 16681 / % possible obs: 94.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.35 | ||||||||||||
Reflection shell | Resolution: 2.48→2.5 Å / Redundancy: 0.76 % / Mean I/σ(I) obs: 4.6 / % possible all: 75.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.866 / SU B: 10.148 / SU ML: 0.227 / Cross valid method: THROUGHOUT / ESU R: 0.607 / ESU R Free: 0.315 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.139 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.564 Å / Total num. of bins used: 20 /
|