[English] 日本語
![](img/lk-miru.gif)
- PDB-3ip0: Crystal structure of E. coli HPPK in complex with MgAMPCPP and 6-... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3ip0 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of E. coli HPPK in complex with MgAMPCPP and 6-hydroxymethylpterin/6-carboxypterin | |||||||||
![]() | 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase | |||||||||
![]() | TRANSFERASE / alpha beta / ATP-binding / Folate biosynthesis / Kinase / Nucleotide-binding | |||||||||
Function / homology | ![]() 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / kinase activity / phosphorylation / magnesium ion binding / ATP binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Blaszczyk, J. / Ji, X. | |||||||||
![]() | ![]() Title: Dynamic roles of arginine residues 82 and 92 of Escherichia coli 6-hydroxymethyl-7,8-dihydroptein pyrophosphokinase: Crystallographic studies Authors: Blaszczyk, J. / Li, Y. / Shi, G. / Yan, H. / Ji, X. #1: ![]() Title: Catalytic center assembly of HPPK as revealed by the crystal structure of a ternary complex at 1.25-angstrom resolution Authors: Blaszczyk, J. / Shi, G. / Yan, H. / Ji, X. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 127.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 99 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 849.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 851.3 KB | Display | |
Data in XML | ![]() | 13.2 KB | Display | |
Data in CIF | ![]() | 20.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1f9hC ![]() 1g4cC ![]() 1hq2C ![]() 1im6C ![]() 1kbrC ![]() 1q0nS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
2 | ![]()
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Components on special symmetry positions |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 17966.535 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P26281, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase |
---|
-Non-polymers , 7 types, 337 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/APC.gif)
![](data/chem/img/HHR.gif)
![](data/chem/img/HHS.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/APC.gif)
![](data/chem/img/HHR.gif)
![](data/chem/img/HHS.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-APC / | #4: Chemical | ChemComp-HHR / | #5: Chemical | ChemComp-HHS / | #6: Chemical | #7: Chemical | ChemComp-ACT / #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.33 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 4000, Ammonium acetate, Sodium acetate, Glycerol., pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 18, 1999 / Details: mirrors |
Radiation | Monochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00928 Å / Relative weight: 1 |
Reflection | Resolution: 0.89→40 Å / Num. all: 100866 / Num. obs: 100866 / % possible obs: 93.1 % / Observed criterion σ(F): -6 / Observed criterion σ(I): -3 / Redundancy: 4.44 % / Biso Wilson estimate: 6.8 Å2 / Rmerge(I) obs: 0.043 / Χ2: 1.003 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 0.89→0.92 Å / Redundancy: 2.74 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 1.73 / Num. unique all: 8139 / Χ2: 1.001 / % possible all: 75.6 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 1Q0N Resolution: 0.89→23.202 Å / Occupancy max: 1 / Occupancy min: 0.17 / SU ML: 0.06 Isotropic thermal model: Anisotropic for fully-occupied non-hydrogen atoms Cross valid method: Throughout before the final 7 cycles of refinement σ(F): 1.35 / Stereochemistry target values: ML Details: The structure was refined for a total of 49 cycles, including 6 cycles with CNS, 20 cycles with SHELXL and 23 cycles with PHENIX
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 75.633 Å2 / ksol: 0.447 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.76 Å2 / Biso mean: 12.849 Å2 / Biso min: 3.12 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.006 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.89→23.202 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
|