+
Open data
-
Basic information
Entry | Database: PDB / ID: 7aaj | ||||||
---|---|---|---|---|---|---|---|
Title | Human porphobilinogen deaminase in complex with cofactor | ||||||
![]() | Porphobilinogen deaminase | ||||||
![]() | TRANSFERASE / PBG-D / Hydroxymethylbilane synthase / HMBS / Porphobilinogen deaminase / heme biosynthesis / porphyria / acute intermittent porphyria | ||||||
Function / homology | ![]() hydroxymethylbilane synthase / hydroxymethylbilane synthase activity / heme B biosynthetic process / heme O biosynthetic process / heme A biosynthetic process / protoporphyrinogen IX biosynthetic process / Heme biosynthesis / heme biosynthetic process / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kallio, J.P. / Bustad, H.J. / Martinez, A. | ||||||
![]() | ![]() Title: Characterization of porphobilinogen deaminase mutants reveals that arginine-173 is crucial for polypyrrole elongation mechanism. Authors: Bustad, H.J. / Kallio, J.P. / Laitaoja, M. / Toska, K. / Kursula, I. / Martinez, A. / Janis, J. #1: ![]() Title: Structural characterization of hydroxymethylbilane synthase mutants associated with acute intermittent porphyria reveals that Arg173 is crucial for the elongation mechanism Authors: Bustad, H.J. / Kallio, J.P. / Laitaoja, M. / Toska, K. / Kursula, I. / Martinez, A. / Janis, J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 173.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 110.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 26.7 KB | Display | |
Data in CIF | ![]() | 36.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7aakC ![]() 3ecrS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
2 | ![]()
| ||||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 39527.141 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: -amino acids 1-2 (GS) in the sample sequence derive from expression tag and biological sequence starts from 3 -Ligand is covalently bound to Cys261 Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1 Details: 25% polyethylene glycol 3350, 200 mM ammonium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→65.08 Å / Num. obs: 69757 / % possible obs: 98.9 % / Redundancy: 7.6 % / Biso Wilson estimate: 34.18 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.095 / Rrim(I) all: 0.102 / Net I/σ(I): 10.24 |
Reflection shell | Resolution: 1.8→1.864 Å / Redundancy: 7.7 % / Rmerge(I) obs: 3.763 / Mean I/σ(I) obs: 0.52 / Num. unique obs: 6877 / CC1/2: 0.54 / Rrim(I) all: 4.028 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3ECR Resolution: 1.8→65.08 Å / SU ML: 0.3198 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 44.5429
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.76 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→65.08 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|