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Yorodumi- PDB-2ftz: Crystal structure of Geranyltranstransferase (EC 2.5.1.10) (tm016... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ftz | ||||||
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Title | Crystal structure of Geranyltranstransferase (EC 2.5.1.10) (tm0161) from THERMOTOGA MARITIMA at 1.90 A resolution | ||||||
Components | geranyltranstransferase | ||||||
Keywords | TRANSFERASE / tm0161 / Geranyltranstransferase (EC 2.5.1.10) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI | ||||||
Function / homology | Function and homology information geranylgeranyl diphosphate biosynthetic process / prenyltransferase activity / farnesyltranstransferase activity Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of Geranyltranstransferase (EC 2.5.1.10) (tm0161) from THERMOTOGA MARITIMA at 1.90 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Remark 999 | SEQUENCE THE PROTEIN WAS REDUCTIVELY METHYLATED PRIOR TO CRYSTALLIZATION. | ||||||
Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ftz.cif.gz | 77.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ftz.ent.gz | 57.3 KB | Display | PDB format |
PDBx/mmJSON format | 2ftz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ftz_validation.pdf.gz | 463.3 KB | Display | wwPDB validaton report |
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Full document | 2ftz_full_validation.pdf.gz | 469.3 KB | Display | |
Data in XML | 2ftz_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 2ftz_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ft/2ftz ftp://data.pdbj.org/pub/pdb/validation_reports/ft/2ftz | HTTPS FTP |
-Related structure data
Related structure data | 1rtrS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE. |
-Components
#1: Protein | Mass: 33180.816 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: tm0161 / Plasmid: MH4a / Production host: Escherichia coli (E. coli) References: GenBank: 4980655, UniProt: Q9WY08*PLUS, (2E,6E)-farnesyl diphosphate synthase | ||||
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#2: Chemical | Num. of mol.: 2 / Source method: obtained synthetically #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.32 Å3/Da / Density % sol: 62.67 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 10.5 Details: 0.2M NaCl, 20.0% PEG-8000, 0.1M CAPS pH 10.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9801 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 10, 2005 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→29.62 Å / Num. obs: 36302 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 7.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1rtr Resolution: 1.9→29.62 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.853 / SU ML: 0.057 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS (2) RESIDUES OF 211-221 WEREN'T VISIBLE IN THE ELECTRON DENSITY MAPS. (3) ADDITIONAL DENSITY FOUND IN THE ACTIVE SITE WAS MODELED AS 2 ...Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS (2) RESIDUES OF 211-221 WEREN'T VISIBLE IN THE ELECTRON DENSITY MAPS. (3) ADDITIONAL DENSITY FOUND IN THE ACTIVE SITE WAS MODELED AS 2 UNKNOWN LIGANDS (UNL). IT WAS NOT POSSIBLE TO UNAMBIGUOUSLY IDENTIFY THE LIGAND WITH THE AVAILABLE DATA. SOME POSSIBILITIES CONSIDERED WERE MULTIPLE CONFORMATIONS OF FPP (FARNESYL DIPHOSPHATE) OR MIXED CONFORMATION WITH DST (DIMETHYLALLYL S-THIOLODIPHOSPHATE), IPR (ISOPENTYL PYROPGOSPHATE) AND FPP. (4) ALL LYSINES ARE METHYLATED EXCEPT LYSINE 2, WHICH IS PROTECTED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.418 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→29.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A
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