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Open data
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Basic information
Entry | Database: PDB / ID: 3k17 | ||||||
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Title | Crystal structure of a Lin0012 protein from Listeria innocua | ||||||
![]() | Lin0012 protein | ||||||
![]() | TRANSFERASE / Lin0012 / Listeria innocua / Protein Structure Initiative II(PSI II) / NYSGXRC / 11277e / Structural Genomics / New York SGX Research Center for Structural Genomics / ATP-binding / Kinase / Nucleotide-binding | ||||||
Function / homology | ![]() phosphomevalonate kinase / phosphomevalonate kinase activity / isopentenyl diphosphate biosynthetic process, mevalonate pathway / ATP binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Palani, K. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
![]() | ![]() Title: Crystal structure of a Lin0012 protein from Listeria innocua Authors: Palani, K. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 282 KB | Display | ![]() |
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PDB format | ![]() | 239.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 475.4 KB | Display | ![]() |
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Full document | ![]() | 508.6 KB | Display | |
Data in XML | ![]() | 55.5 KB | Display | |
Data in CIF | ![]() | 76.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 41128.383 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-PGE / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.76 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2M MgCl2.6H2o, 0.1M HEPES, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 13, 2009 / Details: MIRRORS |
Radiation | Monochromator: SI(III) CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→43.06 Å / Num. all: 105467 / Num. obs: 105467 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.8 % / Biso Wilson estimate: 36.4 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 14.8 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 2.5 / Num. unique all: 10398 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.1098 Å2 / ksol: 0.341125 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→43.06 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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