[English] 日本語
![](img/lk-miru.gif)
- PDB-1tc2: TERNARY SUBSTRATE COMPLEX OF THE HYPOXANTHINE PHOSPHORIBOSYLTRANS... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1tc2 | ||||||
---|---|---|---|---|---|---|---|
Title | TERNARY SUBSTRATE COMPLEX OF THE HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE FROM TRYPANOSOMA CRUZI | ||||||
![]() | PROTEIN (HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE) | ||||||
![]() | TRANSFERASE / GLYCOSYLTRANSFERASE / PHOSPHORIBOSYLTRANSFERASE / NUCLEOTIDE METABOLISM / PURINE SALVAGE / TERNARY COMPLEX / NEAR TRANSITION STATE | ||||||
Function / homology | ![]() hypoxanthine phosphoribosyltransferase / guanine salvage / hypoxanthine metabolic process / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / purine ribonucleoside salvage / nucleotide binding / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Focia, P.J. / Craig III, S.P. / Eakin, A.E. | ||||||
![]() | ![]() Title: Approaching the transition state in the crystal structure of a phosphoribosyltransferase. Authors: Focia, P.J. / Craig III, S.P. / Eakin, A.E. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 95.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 71.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 1tc1S S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.865547, 0.408421, 0.289862), Vector: |
-
Components
-Protein / Sugars , 2 types, 4 molecules AB![](data/chem/img/PRP.gif)
![](data/chem/img/PRP.gif)
#1: Protein | Mass: 25595.404 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q27796, UniProt: Q4DRC4*PLUS, hypoxanthine phosphoribosyltransferase #4: Sugar | |
---|
-Non-polymers , 4 types, 199 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/7HP.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/7HP.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #5: Chemical | ChemComp-MN / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.35 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 4.6 / Details: pH 4.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 4, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→20.6 Å / Num. obs: 33026 / % possible obs: 88.8 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rsym value: 0.051 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 1.81→1.85 Å / Mean I/σ(I) obs: 3.8 / Rsym value: 0.32 / % possible all: 80.1 |
Reflection | *PLUS Rmerge(I) obs: 0.051 |
Reflection shell | *PLUS % possible obs: 80.1 % / Rmerge(I) obs: 0.32 |
-
Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1TC1 Resolution: 1.81→6 Å / Cross valid method: THROUGHOUT / σ(F): 1 Details: PATCH STATEMENTS WERE USED FOR CIS PEPTIDES AND METAL-OXYGEN BONDS SER 88 IS POORLY ORDERED IN SUBUNIT A THE ENERGIES FOR METAL-OXYGEN BOND LENGTHS AND ANGLES WERE SET ARTIFICIALLY LOW ...Details: PATCH STATEMENTS WERE USED FOR CIS PEPTIDES AND METAL-OXYGEN BONDS SER 88 IS POORLY ORDERED IN SUBUNIT A THE ENERGIES FOR METAL-OXYGEN BOND LENGTHS AND ANGLES WERE SET ARTIFICIALLY LOW DURING REFINEMENT IN ORDER TO ALLOW THESE ATOMS MORE FREEDOM TO ADJUST
| ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.81→6 Å
| ||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||
LS refinement shell | Resolution: 1.81→1.85 Å / Total num. of bins used: 15
| ||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
|