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Open data
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Basic information
Entry | Database: PDB / ID: 4aba | ||||||
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Title | Fragments bound to bovine trypsin for the SAMPL challenge | ||||||
![]() | CATIONIC TRYPSIN | ||||||
![]() | HYDROLASE / FRAGMENT SCREENING / MODELLING | ||||||
Function / homology | ![]() trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding 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 |
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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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80 KB | Display | ![]() |
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PDB format | ![]() | 59.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 479.4 KB | Display | ![]() |
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Full document | ![]() | 486 KB | Display | |
Data in XML | ![]() | 16.3 KB | Display | |
Data in CIF | ![]() | 25.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ab8C ![]() 4ab9C ![]() 4abbC ![]() 4abdC ![]() 4abeC ![]() 4abfC ![]() 4abgC ![]() 4abhC ![]() 1k1mS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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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) ![]() ![]() |
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-Non-polymers , 6 types, 368 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/SW1.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/SW1.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-CA / | #4: Chemical | ChemComp-EDO / #5: Chemical | #6: Chemical | ChemComp-SW1 / | #7: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | UNKNOWN LIGAND (UNL): FRAGMENT CC11513 FROM MAYBRIDGE |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 36.1 % / Description: NONE |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 4, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→44 Å / Num. obs: 56922 / % possible obs: 95.7 % / Observed criterion σ(I): 1 / Redundancy: 7.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.9 |
Reflection shell | Resolution: 1.25→1.32 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 7.8 / % possible all: 88.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1K1M Resolution: 1.25→66.69 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.513 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES REFINED INDIVIDUALLY.
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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: 8.886 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→66.69 Å
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Refine LS restraints |
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