+
Open data
-
Basic information
Entry | Database: PDB / ID: 4abe | ||||||
---|---|---|---|---|---|---|---|
Title | Fragments bound to bovine trypsin for the SAMPL challenge | ||||||
![]() | CATIONIC TRYPSIN | ||||||
![]() | ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Newman, J. / Peat, T.S. | ||||||
![]() | ![]() Title: The Dingo Dataset: A Comprehensive Set of Data for the Sampl Challenge. Authors: Newman, J. / Dolezal, O. / Fazio, V. / Caradoc-Davies, T. / Peat, T.S. #1: Journal: J.Biomol.Screen / Year: 2009 Title: Practical Aspects of the Sampl Challenge: Providing an Extensive Experimental Data Set for the Modeling Community. Authors: Newman, J. / Fazio, V.J. / Caradoc-Davies, T.T. / Branson, K. / Peat, T.S. #2: ![]() Title: Fragment Screening for the Modelling Community: Spr, Itc, and Crystallography Authors: Dolezal, O. / Doughty, L. / Hattarki, M.K. / Fazio, V.J. / Caradoc-Davies, T.T. / Newman, J. / Peat, T.S. | ||||||
History |
| ||||||
Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 77.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 57.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 4ab8C ![]() 4ab9C ![]() 4abaC ![]() 4abbC ![]() 4abdC ![]() 4abfC ![]() 4abgC ![]() 4abhC ![]() 1k1mS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SIGMA / Source: (natural) ![]() ![]() ![]() ![]() ![]() |
---|
-Non-polymers , 7 types, 336 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/913.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/913.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ![]() #3: Chemical | ChemComp-CA / | #4: Chemical | ChemComp-EDO / ![]() #5: Chemical | ChemComp-913 / ( | #6: Chemical | ChemComp-DMS / | ![]() #7: Chemical | ChemComp-CL / | ![]() #8: Water | ChemComp-HOH / | ![]() |
---|
-Details
Nonpolymer details | LIGAND (913): FRAGMENT CC32913 FROM MAYBRIDGE |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 36.1 % / Description: NONE |
---|---|
Crystal grow![]() | pH: 5.8 Details: 22.5% PEG 3350, 0.18 M AMMONIUM SULFATE, 0.12 M SODIUM THIOCYANATE, 0.09 M BIS-TRIS PH 5.5, 0.01 M TRIS PH 8.5 (FINAL MEASURED PH=5.82). THE PROTEIN WAS AT 2 MM (47 MG/ML), WITH 4 MM ...Details: 22.5% PEG 3350, 0.18 M AMMONIUM SULFATE, 0.12 M SODIUM THIOCYANATE, 0.09 M BIS-TRIS PH 5.5, 0.01 M TRIS PH 8.5 (FINAL MEASURED PH=5.82). THE PROTEIN WAS AT 2 MM (47 MG/ML), WITH 4 MM BENZYLAMINE AND 10 MM CALCIUM CHLORIDE ADDED TO STABILIZE IT. THE CRYSTALLIZATIONS WERE SET UP WITH A PHOENITO PROTOCOL (NEWMAN ET AL. 2008), WHERE A PHOENIX ROBOT (ART ROBBINS INSTRUMENTS, SUNNYSIDE, CA) WAS USED TO DISPENSE THE PROTEIN INTO AN SD2 CRYSTALLIZATION PLATE (PRE-FILLED WITH 50 ML RESERVOIR SOLUTION) AND A MOSQUITO ROBOT (TTP LABTECH, MELBOURN, UK) WAS USED TO DISPENSE THE RESERVOIR SOLUTION AND SEED STOCK OVER THE PROTEIN DROPLET. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 4, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.3→44 Å / Num. obs: 52662 / % possible obs: 99.5 % / Observed criterion σ(I): 1 / Redundancy: 7.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 1.3→1.37 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 4.5 / % possible all: 98.7 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1K1M Resolution: 1.3→43.97 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 0.645 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 9.109 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→43.97 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|