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Yorodumi- PDB-2djz: Crystal Structure Of Biotin Protein Ligase From Pyrococcus Horiko... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2djz | ||||||
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Title | Crystal Structure Of Biotin Protein Ligase From Pyrococcus Horikoshii OT3 in complex with Biotinyl-5'-AMP, K111A mutation | ||||||
Components | 235aa long hypothetical biotin-[acetyl-CoA-carboxylase] ligase | ||||||
Keywords | LIGASE / Biotin Biosynthesis / Dimer / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information biotin-[acetyl-CoA-carboxylase] ligase activity / protein modification process / ATP binding Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.85 Å | ||||||
Authors | Bagautdinov, B. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Ligand Structures Of Biotin Protein Ligase From Pyrococcus Horikoshii OT3 Authors: Bagautdinov, B. / Kunishima, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2djz.cif.gz | 113.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2djz.ent.gz | 85.9 KB | Display | PDB format |
PDBx/mmJSON format | 2djz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dj/2djz ftp://data.pdbj.org/pub/pdb/validation_reports/dj/2djz | HTTPS FTP |
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-Related structure data
Related structure data | 2deqSC 2dtiC 2hniC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
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: 26045.422 Da / Num. of mol.: 2 / Mutation: K111A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: birA / Plasmid: pET 11a / Production host: Escherichia coli (E. coli) / Strain (production host): (DE3)RIL References: UniProt: O57883, biotin-[biotin carboxyl-carrier protein] ligase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-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: 42.8 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.2 Details: PEG 20000, Acetate, NaOH, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Nov 22, 2005 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→37.43 Å / Num. all: 37673 / Num. obs: 36969 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 20.439 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.071 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 2.37 / Num. unique all: 3523 / Rsym value: 0.3 / % possible all: 92.5 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2DEQ Resolution: 1.85→37.43 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 26.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→37.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.92 Å / Rfactor Rfree error: 0.02
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