[English] 日本語
![](img/lk-miru.gif)
- PDB-5gu9: Structure of biotin carboxyl carrier protein from pyrococcus hori... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5gu9 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of biotin carboxyl carrier protein from pyrococcus horikoshi OT3 (delta N79) A138I mutant | ||||||
![]() | 149aa long hypothetical methylmalonyl-CoA decarboxylase gamma chain | ||||||
![]() | TRANSFERASE / Surface engineering / Crystal packing / Crystal contact engineering | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yamada, K. / Kunishima, N. / Matsuura, Y. / Nakai, K. / Naitow, H. / Fukasawa, Y. / Tomii, K. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() 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: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 29.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 18.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 427.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 427.5 KB | Display | |
Data in XML | ![]() | 6.4 KB | Display | |
Data in CIF | ![]() | 8.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5gu8C ![]() 5guaC ![]() 2evbS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 7742.198 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 80-149 / Mutation: A138I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3 Gene: PH1284 / Plasmid: PET 11A / Production host: ![]() ![]() |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.71 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% PEG 3350, 0.2M magnesium formate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
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: 1.9→38.7 Å / Num. obs: 5180 / % possible obs: 98.8 % / Redundancy: 5.8 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 47.7 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.096 / Mean I/σ(I) obs: 24.3 / % possible all: 99.1 |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2EVB Resolution: 1.9→36.6 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / Phase error: 20.29
| ||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||
Displacement parameters | Biso mean: 19.6 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→36.6 Å
| ||||||||||||||||||||
LS refinement shell | Resolution: 1.9→2.39 Å
|