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Yorodumi- PDB-5gu8: Structure of biotin carboxyl carrier protein from pyrococcus hori... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gu8 | ||||||
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Title | Structure of biotin carboxyl carrier protein from pyrococcus horikoshi OT3 (delta N79) wild type | ||||||
Components | 149aa long hypothetical methylmalonyl-CoA decarboxylase gamma chain | ||||||
Keywords | TRANSFERASE / Surface engineering / Crystal packing / Crystal contact engineering | ||||||
Function / homology | Function and homology information Biotin-binding site / Biotin-requiring enzymes attachment site. / Biotin-requiring enzyme / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Yamada, K. / Kunishima, N. / Matsuura, Y. / Nakai, K. / Naitow, H. / Fukasawa, Y. / Tomii, K. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2017 Title: Designing better diffracting crystals of biotin carboxyl carrier protein from Pyrococcus horikoshii by a mutation based on the crystal-packing propensity of amino acids. Authors: Yamada, K.D. / Kunishima, N. / Matsuura, Y. / Nakai, K. / Naitow, H. / Fukasawa, Y. / Tomii, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gu8.cif.gz | 29.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gu8.ent.gz | 17.5 KB | Display | PDB format |
PDBx/mmJSON format | 5gu8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gu/5gu8 ftp://data.pdbj.org/pub/pdb/validation_reports/gu/5gu8 | HTTPS FTP |
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-Related structure data
Related structure data | 5gu9C 5guaC 2evbS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 7700.118 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 80-149 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (archaea) Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3 Gene: PH1284 / Plasmid: PET 11A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O59021 |
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#2: Chemical | ChemComp-NA / |
#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: 2.08 Å3/Da / Density % sol: 40.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 3.5 M sodium formate, 0.1 M Tris buffer |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→33.2 Å / Num. obs: 6329 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 11.3 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 30.5 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 11.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2EVB Resolution: 1.8→33.2 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / Phase error: 17.34
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||
Displacement parameters | Biso mean: 16.9 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→33.2 Å
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LS refinement shell | Resolution: 1.8→2.27 Å
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