[English] 日本語
Yorodumi- PDB-3q2q: Crystal structure of geranylgeranyl pyrophosphate synthase from C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3q2q | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of geranylgeranyl pyrophosphate synthase from Corynebacterium glutamicum complexed with calcium and isoprenyl diphosphate | ||||||
Components | Geranylgeranyl pyrophosphate synthase | ||||||
Keywords | TRANSFERASE / ISOPRENYL DIPHOSPHATE SYNTHASE / STRUCTURAL GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE / NYSGRC / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / ISOPRENE BIOSYNTHESIS / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS | ||||||
Function / homology | Function and homology information heptaprenyl diphosphate synthase activity / heptaprenyl diphosphate synthase / isoprenoid biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | Corynebacterium glutamicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.9 Å | ||||||
Authors | Patskovsky, Y. / Toro, R. / Rutter, M. / Sauder, J.M. / Poulter, C.D. / Gerlt, J.A. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily. Authors: Wallrapp, F.H. / Pan, J.J. / Ramamoorthy, G. / Almonacid, D.E. / Hillerich, B.S. / Seidel, R. / Patskovsky, Y. / Babbitt, P.C. / Almo, S.C. / Jacobson, M.P. / Poulter, C.D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3q2q.cif.gz | 84.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3q2q.ent.gz | 62.4 KB | Display | PDB format |
PDBx/mmJSON format | 3q2q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3q2q_validation.pdf.gz | 452.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3q2q_full_validation.pdf.gz | 461.7 KB | Display | |
Data in XML | 3q2q_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 3q2q_validation.cif.gz | 23.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q2/3q2q ftp://data.pdbj.org/pub/pdb/validation_reports/q2/3q2q | HTTPS FTP |
-Related structure data
Related structure data | 3lomC 3lvsC 3mzvC 3nf2C 3oyrC 3p41C 3p8lC 3p8rC 3pdeC 3pkoC 3q1oC 3qqvC 3rmgC 3ts7C 3ucaC 4dhdC 4f62C 4fp4C 3lmdS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 39078.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: cg0559, Cgl0473, ispB / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) References: UniProt: Q8NT37, heptaprenyl diphosphate synthase, Transferases; Transferring alkyl or aryl groups, other than methyl groups | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-DMA / | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57.09 % |
---|---|
Crystal grow | Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.1M SODIUM ACETATE, PH 4.5, 30% PEG400, 200MM CALCIUM ACETATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K |
-Data collection
Diffraction | Mean temperature: 93 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9789 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 25, 2010 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. obs: 36231 / % possible obs: 99.8 % / Observed criterion σ(I): -5 / Redundancy: 6.4 % / Biso Wilson estimate: 37.374 Å2 / Rsym value: 0.075 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 0.9 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: molecular replacement Starting model: 3LMD Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.158 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.117 / 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: 51.085 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→40 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
|