+Open data
-Basic information
Entry | Database: PDB / ID: 2bza | ||||||
---|---|---|---|---|---|---|---|
Title | BOVINE PANCREAS BETA-TRYPSIN IN COMPLEX WITH BENZYLAMINE | ||||||
Components | PROTEIN (TRYPSIN) | ||||||
Keywords | HYDROLASE / HYDROLASE (SERINE PROTEINASE) | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Ota, N. / Stroupe, C. / Ferreira-Da-Silva, J.M.S. / Shah, S.S. / Mares-Guia, M. / Brunger, A.T. | ||||||
Citation | Journal: Proteins / Year: 1999 Title: Non-Boltzmann thermodynamic integration (NBTI) for macromolecular systems: relative free energy of binding of trypsin to benzamidine and benzylamine. Authors: Ota, N. / Stroupe, C. / Ferreira-da-Silva, J.M. / Shah, S.A. / Mares-Guia, M. / Brunger, A.T. #1: Journal: J.Mol.Biol. / Year: 1989 Title: Crystal structure of bovine beta-trypsin at 1.5 A resolution in a crystal form with low molecular packing density. Active site geometry, ion pairs and solvent structure. Authors: Bartunik, H.D. / Summers, L.J. / Bartsch, H.H. #2: Journal: Acta Crystallogr.,Sect.B / Year: 1983 Title: The Geometry of the Reactive Site and of the Peptide Groups in Trypsin, Trypsinogen and its Complexes with Inhibitors Authors: Marquart, M. / Walter, J. / Deisenhofer, J. / Bode, W. / Huber, R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2bza.cif.gz | 56.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2bza.ent.gz | 40.2 KB | Display | PDB format |
PDBx/mmJSON format | 2bza.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bza_validation.pdf.gz | 450.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2bza_full_validation.pdf.gz | 453 KB | Display | |
Data in XML | 2bza_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 2bza_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/2bza ftp://data.pdbj.org/pub/pdb/validation_reports/bz/2bza | HTTPS FTP |
-Related structure data
Related structure data | 1ce5C 3ptbS 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 / Source method: isolated from a natural source Details: BOVINE PANCREAS BETA-TRYPSIN PURCHASED FROM WORTHINGTON BIOCHEMICAL CORPORATION Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P00760, trypsin |
---|
-Non-polymers , 5 types, 107 molecules
#2: Chemical | ChemComp-CA / |
---|---|
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-SO4 / |
#5: Chemical | ChemComp-ABN / |
#6: Water | ChemComp-HOH / |
-Details
Has protein modification | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.92 % | ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 6 / Details: pH 6.0 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Aug 1, 1997 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→24 Å / Num. obs: 21208 / % possible obs: 93.4 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 12.9 Å2 / Rsym value: 0.07 / Net I/σ(I): 19.25 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 1.96 % / Mean I/σ(I) obs: 5.1 / Rsym value: 0.201 / % possible all: 84 |
Reflection | *PLUS Lowest resolution: 32 Å / Num. obs: 20938 / % possible obs: 92.2 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.091 |
Reflection shell | *PLUS % possible obs: 86.8 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.347 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3PTB Resolution: 1.9→32 Å / Rfactor Rfree error: 0.004 / Data cutoff high rms absF: 448793.95 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.66 Å2 / ksol: 0.42 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.5 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→32 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 0.3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 32 Å / σ(F): 0 / % reflection Rfree: 9.8 % / Rfactor obs: 0.175 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 22.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.255 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.226 / Num. reflection obs: 1934 |