[English] 日本語
![](img/lk-miru.gif)
- PDB-2x5s: Crystal structure of T. maritima GDP-mannose pyrophosphorylase in... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2x5s | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of T. maritima GDP-mannose pyrophosphorylase in apo state. | ||||||
![]() | MANNOSE-1-PHOSPHATE GUANYLYLTRANSFERASE | ||||||
![]() | TRANSFERASE / NUCLEOTIDYL TRANSFERASE | ||||||
Function / homology | ![]() mannose-1-phosphate guanylyltransferase (GTP) activity / GDP-mannose biosynthetic process / GTP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pelissier, M.C. / Lesley, S. / Kuhn, P. / Bourne, Y. | ||||||
![]() | ![]() Title: Structural Insights Into the Catalytic Mechanism of Bacterial Guanosine-Diphospho-D-Mannose Pyrophosphorylase and its Regulation by Divalent Ions. Authors: Pelissier, M.C. / Lesley, S. / Kuhn, P. / Bourne, Y. | ||||||
History |
| ||||||
Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 145 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 114.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 454.2 KB | Display | |
Data in XML | ![]() | 25.1 KB | Display | |
Data in CIF | ![]() | 34 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2x5zC ![]() 2x60C ![]() 2x65C ![]() 2cu2S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 38655.359 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9X0C3, mannose-1-phosphate guanylyltransferase #2: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, MET 1 TO VAL ENGINEERED RESIDUE IN CHAIN A, VAL 261 TO LEU ...ENGINEERED | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.47 % / Description: NONE |
---|---|
Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 MM PCB PH 7.5, 35% (V/V) MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 1, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→65.37 Å / Num. obs: 31744 / % possible obs: 99.2 % / Observed criterion σ(I): 3.5 / Redundancy: 6 % / Biso Wilson estimate: 59.338 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 2.35→2.48 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.5 / % possible all: 96.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2CU2 Resolution: 2.35→65.37 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.919 / SU B: 23.518 / SU ML: 0.251 / Cross valid method: THROUGHOUT / ESU R: 0.429 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.786 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→65.37 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|