[English] 日本語
Yorodumi- PDB-5gua: Structure of biotin carboxyl carrier protein from pyrococcus hori... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gua | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of biotin carboxyl carrier protein from pyrococcus horikoshi OT3 (delta N79) A138Y mutant | ||||||
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. / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Biotin-requiring enzyme / 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: 1.5 Å | ||||||
Authors | Yamada, K. / Kunishima, N. / Matsuura, Y. / Nakai, K. / Naitow, H. / Fukasawa, Y. / Tomii, K. | ||||||
Funding support | Japan, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5gua.cif.gz | 28.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5gua.ent.gz | 17.6 KB | Display | PDB format |
PDBx/mmJSON format | 5gua.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gu/5gua ftp://data.pdbj.org/pub/pdb/validation_reports/gu/5gua | HTTPS FTP |
---|
-Related structure data
Related structure data | 5gu8C 5gu9C 2evbS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 7792.214 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 80-149 / Mutation: A138Y 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 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.33 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 2.5M sodium chloride, 0.2M lithium sulfate, 0.1M acetate-NaOH |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
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: 1.5→33.8 Å / Num. obs: 11290 / % possible obs: 99.4 % / Redundancy: 9.9 % / Biso Wilson estimate: 10.4 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 41.2 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.102 / Mean I/σ(I) obs: 16 / % possible all: 98.2 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2EVB Resolution: 1.5→33.8 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / Phase error: 21.34
| ||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||
Displacement parameters | Biso mean: 17.8 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→33.8 Å
| ||||||||||||||||||||
LS refinement shell | Resolution: 1.5→1.65 Å
|