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- PDB-3lom: CRYSTAL STRUCTURE OF GERANYLTRANSFERASE FROM Legionella pneumophila -
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Open data
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Basic information
Entry | Database: PDB / ID: 3lom | ||||||
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Title | CRYSTAL STRUCTURE OF GERANYLTRANSFERASE FROM Legionella pneumophila | ||||||
![]() | Geranyltranstransferase | ||||||
![]() | TRANSFERASE / GERANYLTRANSFERASE / 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 | ![]() geranylgeranyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase / farnesyltranstransferase activity / geranyltranstransferase activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Patskovsky, Y. / Toro, R. / Rutter, M. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 124.2 KB | Display | ![]() |
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PDB format | ![]() | 98.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 454.2 KB | Display | ![]() |
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Full document | ![]() | 463.5 KB | Display | |
Data in XML | ![]() | 22.5 KB | Display | |
Data in CIF | ![]() | 31.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3lvsC ![]() 3mzvC ![]() 3nf2C ![]() 3oyrC ![]() 3p41C ![]() 3p8lC ![]() 3p8rC ![]() 3pdeC ![]() 3pkoC ![]() 3q1oC ![]() 3q2qC ![]() 3qqvC ![]() 3rmgC ![]() 3ts7C ![]() 3ucaC ![]() 4dhdC ![]() 4f62C ![]() 4fp4C C: citing same article ( |
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Similar structure data | |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 34775.922 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: ispA, lpg2330 / Production host: ![]() ![]() References: UniProt: Q5ZT35, (2E,6E)-farnesyl diphosphate synthase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.91 % / Description: DATA ANISOTROPIC |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 0.1M PHOSPHATE-CITRATE PH 4.2, 200MM LITHIUM SULFATE, 20% PEG1000, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 23, 2010 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→40 Å / Num. obs: 30725 / % possible obs: 99.9 % / Observed criterion σ(I): -5 / Redundancy: 9.3 % / Rsym value: 0.096 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 61.493 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.301→2.361 Å / Total num. of bins used: 20
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