[English] 日本語
![](img/lk-miru.gif)
- PDB-3no5: Crystal structure of a Pfam DUF849 domain containing protein (Reu... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3no5 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a Pfam DUF849 domain containing protein (Reut_A1631) from Ralstonia eutropha JMP134 at 1.90 A resolution | ||||||
![]() | Uncharacterized protein | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Pfam DUF849 domain containing protein / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | ![]() L-lysine catabolic process to acetate / transferase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) | ||||||
![]() | ![]() Title: Crystal structure of a Pfam DUF849 domain containing protein (Reut_A1631) from Ralstonia eutropha JMP134 at 1.90 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 649.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 540 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 487.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 497.2 KB | Display | |
Data in XML | ![]() | 67.7 KB | Display | |
Data in CIF | ![]() | 96.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3chvS S: Starting model for refinement |
---|---|
Similar structure data | |
Other databases |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 30136.668 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT (1-274) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (1-274) WAS EXPRESSED WITH A PURIFICATI | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.75 % |
---|---|
Crystal grow | Temperature: 277 K / pH: 6.33 Details: 18.0% polyethylene glycol 8000, 0.15M magnesium acetate, 0.1M sodium cacodylate pH 6.33, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 12, 2007 / Details: FLAT MIRROR (VERTICAL FOCUSING) |
Radiation | Monochromator: SINGLE CRYSTAL SI(111) BENT MONOCHROMATOR (HORIZONTAL FOCUSING) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91162 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→29.961 Å / Num. obs: 143033 / % possible obs: 99.9 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.124 / Rsym value: 0.124 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.436 / % possible all: 100 |
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3CHV Resolution: 1.9→29.96 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.893 / Occupancy max: 1 / Occupancy min: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 Details: (1). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION.0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (2). ...Details: (1). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION.0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (2). THE MODELING OF ZINC IS SUPPORTED BY ANOMALOUS DIFFERENCE MAPS AND STRUCTURAL SIMILARITY TO A HOMOLOG, PDB ID 3CHV. (3).ACETATE (ACT) FROM THE CRYSTALLIZATION AND ETHYLENE GLYCOL(EDO) USED AS A CRYOPROTECTANT WERE MODELED INTO THE STRUCTURE.(4). ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. (5). ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. (6). WATERS WERE EXCLUDED FROM TLS ASSIGNMENT.
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.69 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→29.96 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|