[English] 日本語
Yorodumi- PDB-3smp: Monoclinic crystal structure of human pantothenate kinase 1 alpha -
+Open data
-Basic information
Entry | Database: PDB / ID: 3smp | ||||||
---|---|---|---|---|---|---|---|
Title | Monoclinic crystal structure of human pantothenate kinase 1 alpha | ||||||
Components | Pantothenate kinase 1 | ||||||
Keywords | TRANSFERASE / Structural Genomics Consortium / SGC / structural genomics | ||||||
Function / homology | Function and homology information Coenzyme A biosynthesis / acetyl-CoA binding / pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / clathrin-coated vesicle / recycling endosome / phosphorylation / nucleolus / protein homodimerization activity ...Coenzyme A biosynthesis / acetyl-CoA binding / pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / clathrin-coated vesicle / recycling endosome / phosphorylation / nucleolus / protein homodimerization activity / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.9 Å | ||||||
Authors | Guan, X. / Tempel, W. / Hong, B. / Wernimont, A.K. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Park, H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: to be published Title: Monoclinic crystal structure of human pantothenate kinase 1 alpha Authors: Guan, X. / Tempel, W. / Hong, B. / Wernimont, A.K. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Park, H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3smp.cif.gz | 303 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3smp.ent.gz | 245.3 KB | Display | PDB format |
PDBx/mmJSON format | 3smp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3smp_validation.pdf.gz | 855.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3smp_full_validation.pdf.gz | 863.8 KB | Display | |
Data in XML | 3smp_validation.xml.gz | 29 KB | Display | |
Data in CIF | 3smp_validation.cif.gz | 40.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sm/3smp ftp://data.pdbj.org/pub/pdb/validation_reports/sm/3smp | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 43072.340 Da / Num. of mol.: 2 / Fragment: UNP residues 231-597 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PANK1, PANK / Plasmid: BL21-V2R / Production host: Escherichia coli (E. coli) / Strain (production host): pET28-LIC / References: UniProt: Q8TE04, pantothenate kinase |
---|
-Non-polymers , 5 types, 142 molecules
#2: Chemical | ChemComp-ARS / #3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-UNX / #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 55.8 % |
---|---|
Crystal grow | Method: vapor diffusion, sitting drop / pH: 5.5 Details: 20% peg-1500, 0.2 M magnesium chloride, 0.1 M sodium cacodylate, pH 5.5, vapor diffusion, sitting drop |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 23, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→50 Å / Num. obs: 69596 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 40.647 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 11.65 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / Matrix type: sparse / WRfactor Rfree: 0.249 / WRfactor Rwork: 0.215 / Occupancy max: 1 / Occupancy min: 0.01 / SU B: 8.955 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED. Cofactor geometry restraints are based on pdb entry 3R95 and were optimized on the prodrg server. coot, phenix, ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED. Cofactor geometry restraints are based on pdb entry 3R95 and were optimized on the prodrg server. coot, phenix, arp/warp, buccaneer and the molprobity server were also used during refinement. THE ELECTRON DENSITY and peaks in the anomalous difference fourier map SUGGEST THE MODIFICATION OF THE SULFHYDRYL GROUPS OF some cystyl residues, POSSIBLY BY A REACTION with CACODYLATE, SIMILAR TO SCOTT ET AL (1993, CHEM RES REMARK 600 TOXICOL 6:102) AND GOLDGUR ET AL (1998, PROC NATL ACAD SCI USA 95:9150). ONLY THE PUTATIVE ARSENIC ATOMS OF THE MODIFICATION HAVE BEEN MODELED. Sulfur-arsenic bonds were poorly restrained and their lengths are not reliable.
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.89 Å2 / Biso mean: 31.841 Å2 / Biso min: 18.19 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|