[English] 日本語
![](img/lk-miru.gif)
- PDB-6g74: Structure of the Y21F variant of quinolinate synthase in complex ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6g74 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the Y21F variant of quinolinate synthase in complex with phthalate | ||||||
![]() | Quinolinate synthase A | ||||||
![]() | TRANSFERASE / NAD BIOSYNTHESIS / IRON SULFUR CLUSTER | ||||||
Function / homology | ![]() quinolinate synthase / quinolinate synthetase A activity / 'de novo' NAD biosynthetic process from aspartate / 4 iron, 4 sulfur cluster binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Volbeda, A. / Fontecilla-Camps, J.C. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Crystallographic Trapping of Reaction Intermediates in Quinolinic Acid Synthesis by NadA. Authors: Volbeda, A. / Saez Cabodevilla, J. / Darnault, C. / Gigarel, O. / Han, T.H. / Renoux, O. / Hamelin, O. / Ollagnier-de-Choudens, S. / Amara, P. / Fontecilla-Camps, J.C. #1: ![]() Title: Crystal Structures of Quinolinate Synthase in Complex with a Substrate Analogue, the Condensation Intermediate, and Substrate-Derived Product. Authors: Volbeda, A. / Darnault, C. / Renoux, O. / Reichmann, D. / Amara, P. / Ollagnier de Choudens, S. / Fontecilla-Camps, J.C. #2: ![]() Title: The crystal structure of Fe4S4 quinolinate synthase unravels an enzymatic dehydration mechanism that uses tyrosine and a hydrolase-type triad. Authors: Cherrier, M.V. / Chan, A. / Darnault, C. / Reichmann, D. / Amara, P. / Ollagnier de Choudens, S. / Fontecilla-Camps, J.C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 220.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 175.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 470.8 KB | Display | |
Data in XML | ![]() | 28.9 KB | Display | |
Data in CIF | ![]() | 43 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6f48C ![]() 6f4dC ![]() 6f4lC ![]() 4p3xS ![]() 5lqmS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 34509.402 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: nadA, TM_1644 / Plasmid: PT7 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.13 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: PEG3350, TRIS, KCL, HEPES, PHTHALATE, Na2HPO4, ANAEROBIC |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 30, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97242 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2→49.13 Å / Num. obs: 34665 / % possible obs: 90.2 % / Redundancy: 2.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.044 / Rrim(I) all: 0.072 / Net I/σ(I): 12.1 / Num. measured all: 82582 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4P3X (OPEN FORM) AND 5LQM (CLOSED FORM) Resolution: 2→43.43 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / SU B: 7.989 / SU ML: 0.172 / SU R Cruickshank DPI: 0.3231 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.323 / ESU R Free: 0.21 Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 78.59 Å2 / Biso mean: 31.326 Å2 / Biso min: 14.51 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→43.43 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|