[English] 日本語
Yorodumi- PDB-4ncy: In situ trypsin crystallized on a MiTeGen micromesh with imidazol... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ncy | ||||||
---|---|---|---|---|---|---|---|
Title | In situ trypsin crystallized on a MiTeGen micromesh with imidazole ligand | ||||||
Components | Cationic trypsin | ||||||
Keywords | HYDROLASE / IMIDAZOLE | ||||||
Function / homology | Function and homology information 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 | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å | ||||||
Authors | Yin, X. / Scalia, A. / Leroy, L. / Cuttitta, C.M. / Polizzo, G.M. / Ericson, D.L. / Roessler, C.G. / Campos, O. / Agarwal, R. / Allaire, M. ...Yin, X. / Scalia, A. / Leroy, L. / Cuttitta, C.M. / Polizzo, G.M. / Ericson, D.L. / Roessler, C.G. / Campos, O. / Agarwal, R. / Allaire, M. / Orville, A.M. / Jackimowicz, R. / Ma, M.Y. / Sweet, R.M. / Soares, A.S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Hitting the target: fragment screening with acoustic in situ co-crystallization of proteins plus fragment libraries on pin-mounted data-collection micromeshes. Authors: Yin, X. / Scalia, A. / Leroy, L. / Cuttitta, C.M. / Polizzo, G.M. / Ericson, D.L. / Roessler, C.G. / Campos, O. / Ma, M.Y. / Agarwal, R. / Jackimowicz, R. / Allaire, M. / Orville, A.M. / ...Authors: Yin, X. / Scalia, A. / Leroy, L. / Cuttitta, C.M. / Polizzo, G.M. / Ericson, D.L. / Roessler, C.G. / Campos, O. / Ma, M.Y. / Agarwal, R. / Jackimowicz, R. / Allaire, M. / Orville, A.M. / Sweet, R.M. / Soares, A.S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4ncy.cif.gz | 71.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4ncy.ent.gz | 51.1 KB | Display | PDB format |
PDBx/mmJSON format | 4ncy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ncy_validation.pdf.gz | 472.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4ncy_full_validation.pdf.gz | 478.3 KB | Display | |
Data in XML | 4ncy_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 4ncy_validation.cif.gz | 26.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nc/4ncy ftp://data.pdbj.org/pub/pdb/validation_reports/nc/4ncy | HTTPS FTP |
-Related structure data
Related structure data | 4n8zC 4i8gS S: Starting model for refinement C: citing same article (ref.) |
---|---|
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 / Fragment: UNP residues 24-246 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin |
---|
-Non-polymers , 6 types, 431 molecules
#2: Chemical | ChemComp-CA / | ||||||
---|---|---|---|---|---|---|---|
#3: Chemical | ChemComp-BEN / | ||||||
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-IMD / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.42 % |
---|---|
Crystal grow | Temperature: 277 K / Method: in situ crystallization on micromesh / pH: 7 Details: 30mg/ml+10mg/ml Benzenmidine in 20mM HEPES pH 7 and 10mM CaCl2; precipitant is 20% PEG 8000 + 200mM AmSO4 + 100mM Bis-Tris, In situ crystallization on micromesh, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 4, 2013 |
Radiation | Monochromator: 1.1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→43.77 Å / Num. all: 38208 / Num. obs: 38155 / % possible obs: 99.86 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 5.9 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 46.31 |
Reflection shell | Highest resolution: 1.42 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.043 / Mean I/σ(I) obs: 46.31 / Num. unique all: 38208 / % possible all: 99.86 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4I8G Resolution: 1.42→43.77 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.644 / SU ML: 0.026 / 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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 10.881 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.42→43.77 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.423→1.46 Å / Total num. of bins used: 20
|