+
Open data
-
Basic information
Entry | Database: PDB / ID: 4bcs | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of an avidin mutant | ||||||
![]() | CHIMERIC AVIDIN | ||||||
![]() | BIOTIN-BINDING PROTEIN / LIGAND BINDING | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Airenne, T.T. / Niederhauser, B. / Hytonen, V.P. / Kulomaa, M.S. / Johnson, M.S. | ||||||
![]() | ![]() Title: A Novel Chimeric Avidin with Increased Thermal Stability Using DNA Shuffling. Authors: Taskinen, B. / Airenne, T.T. / Janis, J. / Rahikainen, R. / Johnson, M.S. / Kulomaa, M.S. / Hytonen, V.P. #1: Journal: J.Biotechnol. / Year: 2012 Title: DNA Family Shuffling within the Chicken Avidin Protein Family - a Shortcut to More Powerful Protein Tools. Authors: Niederhauser, B. / Siivonen, J. / Maatta, J.A. / Janis, J. / Kulomaa, M.S. / Hytonen, V.P. | ||||||
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 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-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 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 65 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 47.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 477.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 479.5 KB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 17.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1wbiS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
| ||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.22495, -0.97432, -0.0098), Vector: |
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 13922.716 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|
-Non-polymers , 5 types, 118 molecules ![](data/chem/img/ACT.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/BTN.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/BTN.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ACT / | ||||
---|---|---|---|---|---|
#3: Chemical | ChemComp-PEG / | ||||
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | PRODUCED USING A DNA FAMILY SHUFFLING METHOD WITH GENES OF UNIPROT ENTRIES P02701 AND P56734 |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41 % Description: THE POLYPEPTIDE CHAIN A OF 1WBI WAS USED IN MOLECULAR REPLACEMENT. |
---|---|
Crystal grow | Method: vapor diffusion Details: 300 NL OF PROTEIN SOLUTION (7.36 MG PER ML; 50 MM SODIUM ACETATE, PH 4) WERE MIXED WITH 300 NL OF WELL SOLUTION (0.09 M PHOSPHATE, CITRATE, PH 4.2; 36% PEG 300). VAPOUR DIFFUSION WAS USED. ...Details: 300 NL OF PROTEIN SOLUTION (7.36 MG PER ML; 50 MM SODIUM ACETATE, PH 4) WERE MIXED WITH 300 NL OF WELL SOLUTION (0.09 M PHOSPHATE, CITRATE, PH 4.2; 36% PEG 300). VAPOUR DIFFUSION WAS USED. BEFORE CRYSTALLIZATION, BIOTIN SOLUTION (1 MG PER ML; 5 MM TRIS, PH 8.8 AND 8 MM CHES, PH 9.5) WAS ADDED TO THE PROTEIN SOLUTION IN 1 TO 10 (VOLUME PER VOLUME) RATIO, RESPECTIVELY. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 25, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 22157 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 30 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 5 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1WBI Resolution: 1.8→19.6 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.864 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.475 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→19.6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|