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- PDB-3lwg: Crystal structure of HP0420-homologue C46A from helicobacter felis -
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Open data
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Basic information
Entry | Database: PDB / ID: 3lwg | ||||||
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Title | Crystal structure of HP0420-homologue C46A from helicobacter felis | ||||||
![]() | HP0420 homologue | ||||||
![]() | UNKNOWN FUNCTION / Helicobacter / hotdog-fold / structural genomics | ||||||
Function / homology | Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / membrane => GO:0016020 / Roll / Alpha Beta / HP0420 homologue![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ha, N.-C. / Piao, S. | ||||||
![]() | ![]() Title: Crystal structure and functional insight of HP0420-homolog from Helicobacter felis Authors: Piao, S. / Jin, X.L. / Yun, B.-Y. / Kim, N. / Cho, H.-S. / Fukuda, M. / Lee, H. / Ha, N.-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 | ![]() | 63.7 KB | Display | ![]() |
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PDB format | ![]() | 46.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.6 KB | Display | ![]() |
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Full document | ![]() | 436.4 KB | Display | |
Data in XML | ![]() | 12.9 KB | Display | |
Data in CIF | ![]() | 17.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3lw3SC S: Starting model for refinement 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
#1: Protein | Mass: 16066.624 Da / Num. of mol.: 2 / Mutation: C46A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEB | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 37.07 % |
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Crystal grow | Temperature: 287 K / Method: evaporation / pH: 6.5 Details: 0.01M Cobalt(II)chloride hexahydrate, 0.1M MES pH6.5, 1.8M ammonium sulfate., EVAPORATION, temperature 287K |
-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 1, 2009 / Details: Double mirror |
Radiation | Monochromator: Double mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 23917 / Num. obs: 23847 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Biso Wilson estimate: 10.6 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 30.5 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1165 / Rsym value: 0.318 / % possible all: 99.4 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3LW3 Resolution: 1.8→48.52 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 49922.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.9767 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→48.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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