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- PDB-1kp9: Crystal structure of mycolic acid cyclopropane synthase CmaA1, ap... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kp9 | ||||||
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Title | Crystal structure of mycolic acid cyclopropane synthase CmaA1, apo-form | ||||||
![]() | CYCLOPROPANE-FATTY-ACYL-PHOSPHOLIPID SYNTHASE 1 | ||||||
![]() | TRANSFERASE / mixed alpha beta fold / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC | ||||||
Function / homology | ![]() cyclopropane-fatty-acyl-phospholipid synthase / cyclopropane-fatty-acyl-phospholipid synthase activity / mycolic acid biosynthetic process / S-adenosylmethionine metabolic process / lipid biosynthetic process / methylation / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Huang, C.-C. / Smith, C.V. / Jacobs Jr., W.R. / Glickman, M.S. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC) | ||||||
![]() | ![]() Title: Crystal structures of mycolic acid cyclopropane synthases from Mycobacterium tuberculosis Authors: Huang, C.-C. / Smith, C.V. / Glickman, M.S. / Jacobs Jr., W.R. / Sacchettini, J.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121.1 KB | Display | ![]() |
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PDB format | ![]() | 94.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 384.5 KB | Display | ![]() |
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Full document | ![]() | 398.3 KB | Display | |
Data in XML | ![]() | 13.6 KB | Display | |
Data in CIF | ![]() | 20.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1kpgC ![]() 1kphC ![]() 1kpiC ![]() 1l1eC C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 32497.176 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q11195, UniProt: P9WPB7*PLUS, cyclopropane-fatty-acyl-phospholipid 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: 2.08 Å3/Da / Density % sol: 40.81 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: evaporation / pH: 6.5 Details: PEG 4000, sodium acetate, MES , ammonium acetate, 1,6-hexadiol, pH 6.5, EVAPORATION at 292K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 19 ℃ / Method: batch method | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Feb 15, 2001 / Details: osmic mirrors |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. all: 23312 / Num. obs: 23312 / % possible obs: 87.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.94 % / Biso Wilson estimate: 20.8 Å2 / Rsym value: 0.062 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 2.2→2.34 Å / Mean I/σ(I) obs: 4.3 / Rsym value: 0.183 / % possible all: 73.2 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 45181 / Rmerge(I) obs: 0.062 |
Reflection shell | *PLUS % possible obs: 73.2 % / Rmerge(I) obs: 0.183 |
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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: 29.267 Å2 / ksol: 0.295527 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.21→29.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 30 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.2 / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 36.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.304 / % reflection Rfree: 9.1 % / Rfactor Rwork: 0.242 |