[English] 日本語
![](img/lk-miru.gif)
- PDB-7o87: Crystal structure of holo-F210W mutant of Hydroxy ketone aldolase... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7o87 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of holo-F210W mutant of Hydroxy ketone aldolase (SwHKA) from Sphingomonas wittichii RW1 in complex with hydroxypyruvate | ||||||
![]() | HpcH/HpaI aldolase | ||||||
![]() | LYASE / Class II Pyruvate Aldolase / Metal dependent / Aldol Reaction / Hydroxypyruvate / Pyruvate / holo / Aldolase / Carbon bond formation | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Laustsen, J. / Justo, I. / Marsden, S.R. / Hanefeld, U. / Bento, I. | ||||||
![]() | ![]() Title: Substrate Induced Movement of the Metal Cofactor between Active and Resting State. Authors: Marsden, S.R. / Wijma, H.J. / Mohr, M.K.F. / Justo, I. / Hagedoorn, P.L. / Laustsen, J. / Jeffries, C.M. / Svergun, D. / Mestrom, L. / McMillan, D.G.G. / Bento, I. / Hanefeld, U. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 206.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 23.1 KB | Display | |
Data in CIF | ![]() | 33.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7nnkC ![]() 7nr1C ![]() 7nujC ![]() 7o5iC ![]() 7o5rC ![]() 7o5vC ![]() 7o5wC ![]() 7o9rC ![]() 7obuC ![]() 8adqC ![]() 6r62S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||
Components on special symmetry positions |
|
-
Components
-Protein , 1 types, 2 molecules AAABBB
#1: Protein | Mass: 26823.561 Da / Num. of mol.: 2 / Mutation: F210W Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: RW1 / DSM 6014 / JCM 10273 / Gene: Swit_5035 / Production host: ![]() ![]() |
---|
-Non-polymers , 6 types, 333 molecules ![](data/chem/img/3PY.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.16 % |
---|---|
Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: HEPES, Sodium Citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 3, 2019 | ||||||||||||||||||||||||
Radiation | Monochromator: Oxforf-FNB / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.5→73.97 Å / Num. obs: 65270 / % possible obs: 98.2 % / Redundancy: 3.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.098 / Rrim(I) all: 0.148 / Net I/σ(I): 6 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6R62 Resolution: 1.5→53.731 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.167 / SU ML: 0.076 / Cross valid method: FREE R-VALUE / ESU R: 0.086 / ESU R Free: 0.09 Details: Hydrogens have been added in their riding positions
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.909 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→53.731 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|