+Open data
-Basic information
Entry | Database: PDB / ID: 3caa | |||||||||
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Title | CLEAVED ANTICHYMOTRYPSIN A347R | |||||||||
Components | (ANTICHYMOTRYPSIN) x 2 | |||||||||
Keywords | SERPIN / SERINE PROTEASE INHIBITOR / ANTICHYMOTRYPSIN | |||||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 2.4 Å | |||||||||
Authors | Lukacs, C.M. / Christianson, D.W. | |||||||||
Citation | Journal: Biochemistry / Year: 1998 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: Journal: To be Published 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3caa.cif.gz | 85.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3caa.ent.gz | 64.5 KB | Display | PDB format |
PDBx/mmJSON format | 3caa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ca/3caa ftp://data.pdbj.org/pub/pdb/validation_reports/ca/3caa | HTTPS FTP |
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-Related structure data
Related structure data | 1as4C 4caaC 2caa S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-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.) Homo sapiens (human) / Gene: ACT / Plasmid: PZMS / Gene (production host): ACT / Production host: Escherichia coli (E. coli) / References: UniProt: P01011 |
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#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.) Homo sapiens (human) / Gene: ACT / Plasmid: PZMS / Gene (production host): ACT / Production host: Escherichia coli (E. coli) / References: UniProt: P01011 |
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55 % | ||||||||||||||||||||||||||||||||||||||||
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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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 1.54 |
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 |
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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.
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Displacement parameters | Biso mean: 35.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.51 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.19 / Rfactor Rfree: 0.28 / Rfactor Rwork: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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