+
Open data
-
Basic information
Entry | Database: PDB / ID: 3caa | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | CLEAVED ANTICHYMOTRYPSIN A347R | |||||||||
![]() | (ANTICHYMOTRYPSIN) x 2 | |||||||||
![]() | SERPIN / SERINE PROTEASE INHIBITOR / ANTICHYMOTRYPSIN | |||||||||
Function / homology | ![]() maintenance of gastrointestinal epithelium / regulation of lipid metabolic process / platelet alpha granule lumen / acute-phase response / serine-type endopeptidase inhibitor activity / azurophil granule lumen / Platelet degranulation / secretory granule lumen / collagen-containing extracellular matrix / blood microparticle ...maintenance of gastrointestinal epithelium / regulation of lipid metabolic process / platelet alpha granule lumen / acute-phase response / serine-type endopeptidase inhibitor activity / azurophil granule lumen / Platelet degranulation / secretory granule lumen / collagen-containing extracellular matrix / blood microparticle / inflammatory response / Neutrophil degranulation / DNA binding / extracellular space / extracellular exosome / extracellular region / nucleus Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Lukacs, C.M. / Christianson, D.W. | |||||||||
![]() | ![]() Title: Engineering an anion-binding cavity in antichymotrypsin modulates the "spring-loaded" serpin-protease interaction. Authors: Lukacs, C.M. / Rubin, H. / Christianson, D.W. #1: ![]() Title: Burial of an Ion Pair in the Hydrophobic Core of Cleaved Ala-349->Arg Antichymotrypsin Compromises But Does not Obliterate Serpin Function Authors: Lukacs, C.M. / Rubin, H. / Christianson, D.W. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 85.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 64.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 1as4C ![]() 4caaC ![]() 2caa S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 38612.148 Da / Num. of mol.: 1 / Mutation: A347R Source method: isolated from a genetically manipulated source Details: CLEAVED ANTICHYMOTRYPSIN / Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Protein/peptide | Mass: 4359.141 Da / Num. of mol.: 1 / Mutation: A347R Source method: isolated from a genetically manipulated source Details: CLEAVED ANTICHYMOTRYPSIN / Source: (gene. exp.) ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
Compound details | A: N-TERMINUS TO CLEAVAGE SITE (RESIDUES 20 - 358) B: CLEAVAGE SITE TO C-TERMINUS (RESIDUES 359 - ...A: N-TERMINUS TO CLEAVAGE SITE (RESIDUES 20 - 358) B: CLEAVAGE SITE TO C-TERMINUS (RESIDUES 359 - 393) RESIDUE A 347 IS MUTATION OF ALA->ARG. THIS RESIDUE IS COMPLETELY |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55 % | ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 5.6 Details: 10% PEG MONOMETHYLETHER 5000 0.2 M MAGNESIUM ACETATE 0.1 M SODIUM CITRATE PH 5.6 PROTEIN AT 3 MG/ML | ||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Lukacs, C.M., (1996) Nat.Struct.Biol., 3, 888. | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM / Detector: CCD / Date: Sep 1, 1996 |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 15560 / % possible obs: 83.7 % / Redundancy: 4.05 % / Rsym value: 0.101 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.4 % / Rsym value: 0.399 / % possible all: 85.6 |
Reflection | *PLUS Num. measured all: 63094 / Rmerge(I) obs: 0.101 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: PDB ENTRY 2CAA ![]() 2caa Resolution: 2.4→20 Å / Rfactor Rfree error: 0.0115 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2 Details: ASN A 104 - GLU A 109 ARE IN POOR ELECTRON DENSITY AND SHOULD BE TREATED AS SUCH.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.51 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.19 / Rfactor Rfree: 0.28 / Rfactor Rwork: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|