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Yorodumi- PDB-3lhh: The crystal structure of CBS domain protein from Shewanella oneid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lhh | ||||||
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Title | The crystal structure of CBS domain protein from Shewanella oneidensis MR-1. | ||||||
Components | CBS domain protein | ||||||
Keywords | MEMBRANE PROTEIN / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG / Cell membrane / Transmembrane | ||||||
Function / homology | Function and homology information flavin adenine dinucleotide binding / membrane => GO:0016020 / plasma membrane Similarity search - Function | ||||||
Biological species | Shewanella oneidensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å | ||||||
Authors | Tan, K. / Kagan, O. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of CBS domain protein from Shewanella oneidensis MR-1. Authors: Tan, K. / Kagan, O. / Savchenko, A. / Edwards, A. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lhh.cif.gz | 62.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lhh.ent.gz | 49.9 KB | Display | PDB format |
PDBx/mmJSON format | 3lhh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lhh_validation.pdf.gz | 820.8 KB | Display | wwPDB validaton report |
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Full document | 3lhh_full_validation.pdf.gz | 823.1 KB | Display | |
Data in XML | 3lhh_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | 3lhh_validation.cif.gz | 9.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lh/3lhh ftp://data.pdbj.org/pub/pdb/validation_reports/lh/3lhh | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Experimentally unknown. The chain A is likely a monomer. |
-Components
#1: Protein | Mass: 19594.697 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_2815 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8EDE1 |
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#2: Chemical | ChemComp-AMP / |
#3: 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: 2.15 Å3/Da / Density % sol: 42.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1M Tri-Na-Citrate, 2% MPD, 25% PEG3350, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 2, 2009 / Details: mirror |
Radiation | Monochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97937 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→27.6 Å / Num. all: 10353 / Num. obs: 10353 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 28.1 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.797 / Mean I/σ(I) obs: 1.52 / Num. unique all: 508 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.1→27.578 Å / SU ML: 0.26 / σ(F): 0.08 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.805 Å2 / ksol: 0.332 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→27.578 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Selection details: chain A resid 53:113 |