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Yorodumi- PDB-3hut: Crystal structure of a putative branched-chain amino acid ABC tra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hut | ||||||
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Title | Crystal structure of a putative branched-chain amino acid ABC transporter from Rhodospirillum rubrum | ||||||
Components | putative branched-chain amino acid ABC transporter | ||||||
Keywords | TRANSPORT PROTEIN / Extracellular ligand-binding receptor / Receptor or Singnal protein / 11236m / PSI-2 / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS / NYSGXRC / Protein Structure Initiative / Receptor | ||||||
Function / homology | Leucine-binding protein domain / Periplasmic binding protein / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Extracellular ligand-binding receptor Function and homology information | ||||||
Biological species | Rhodospirillum rubrum ATCC 11170 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.93 Å | ||||||
Authors | Satyanarayana, L. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a putative branched-chain amino acid ABC transporter from Rhodospirillum rubrum Authors: Satyanarayana, L. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hut.cif.gz | 82.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hut.ent.gz | 64.1 KB | Display | PDB format |
PDBx/mmJSON format | 3hut.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hu/3hut ftp://data.pdbj.org/pub/pdb/validation_reports/hu/3hut | HTTPS FTP |
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-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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-Components
#1: Protein | Mass: 38694.480 Da / Num. of mol.: 1 / Fragment: residues 40-386 Source method: isolated from a genetically manipulated source Details: TOP10(Invitrogen) Source: (gene. exp.) Rhodospirillum rubrum ATCC 11170 (bacteria) Strain: ATCC 11170 or NCIB 8255 / Gene: Rru_A2873 / Plasmid: BC-pSGX3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2RQC5 |
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#2: 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: 2.09 Å3/Da / Density % sol: 41.12 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 200mM Magnesium Acetate tetrahydrate + 100mM Sodium Cacodylate pH 6.5 + 20% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 8, 2008 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→50 Å / Num. all: 23896 / Num. obs: 23896 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 8.2 Å2 / Rsym value: 0.083 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 1.93→2 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 5.5 / Num. unique all: 2347 / Rsym value: 0.354 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.93→40.24 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 14.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.93→40.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.93→2.05 Å / Rfactor Rfree error: 0.024
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