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- PDB-4caa: CLEAVED ANTICHYMOTRYPSIN T345R -

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Basic information

Entry
Database: PDB / ID: 4caa
TitleCLEAVED ANTICHYMOTRYPSIN T345R
Components(ANTICHYMOTRYPSIN) x 2
KeywordsSERPIN / 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
Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily ...Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Alpha-1-antichymotrypsin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 2.9 Å
AuthorsLukacs, 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
DepositionAug 14, 1997Processing site: BNL
SupersessionFeb 25, 1998ID: 1CT3
Revision 1.0Feb 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 700SHEET RESIDUE A 345 IS MUTATION OF THR->ARG. THERE IS AN UNUSUAL TWIST TO THE BETA SHEET IN THIS ...SHEET RESIDUE A 345 IS MUTATION OF THR->ARG. THERE IS AN UNUSUAL TWIST TO THE BETA SHEET IN THIS AREA TO KEEP THE ARG SOLVENT EXPOSED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANTICHYMOTRYPSIN
B: ANTICHYMOTRYPSIN


Theoretical massNumber of molelcules
Total (without water)42,9412
Polymers42,9412
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-34 kcal/mol
Surface area15420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.830, 83.510, 82.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ANTICHYMOTRYPSIN / ACT


Mass: 38582.125 Da / Num. of mol.: 1 / Mutation: T345R
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
#2: Protein/peptide ANTICHYMOTRYPSIN / ACT


Mass: 4359.141 Da / Num. of mol.: 1 / Mutation: T345R
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
Compound detailsA: N-TERMINUS TO CLEAVAGE SITE (RESIDUES 20 - 358) B: CLEAVAGE SITE TO C-TERMINUS (RESIDUES 359 - 393)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59 %
Crystal growpH: 5.6
Details: 14% PEG 8000 0.2 M MAGNESIUM ACETATE 0.1 M SODIUM CITRATE PH 5.6
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
IDConc.Common nameCrystal-IDSol-ID
12 mg/mlprotein1drop
25.7 %PEG80001drop
30.07 Mmagnesium acetate1drop
40.03 Msodium citrate1drop
515 %PEG80001reservoir
60.2 Mmagnesium acetate1reservoir
70.1 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 1.54
DetectorType: ADSC / Detector: CCD / Date: Sep 1, 1996
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 37763 / % possible obs: 95.9 % / Redundancy: 3.35 % / Rsym value: 0.085 / Net I/σ(I): 7.1
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.3 % / Rsym value: 0.426 / % possible all: 97.1
Reflection
*PLUS
Num. obs: 11269 / Num. measured all: 37763 / Rmerge(I) obs: 0.085

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 1CT3

1ct3
PDB Unreleased entry


Resolution: 2.9→8 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2
Details: GLN A 105 - ASP A 108 ARE IN VERY POOR ELECTRON DENSITY AND SHOULD BE TREATED AS SUCH. THEY HAVE BEEN REFINED WITH OCCUPANCIES OF 0.0. DATA WAS INDEXED WITH B>C IN ORDER TO USE DIFFERENCE ...Details: GLN A 105 - ASP A 108 ARE IN VERY POOR ELECTRON DENSITY AND SHOULD BE TREATED AS SUCH. THEY HAVE BEEN REFINED WITH OCCUPANCIES OF 0.0. DATA WAS INDEXED WITH B>C IN ORDER TO USE DIFFERENCE FOURIER TECHNIQUES FROM ENTRY 1CT3. THE DIFFERENCE IN UNIT CELLS IS PRESUMABLY DUE TO CRYOGENIC TECHNIQUE USED IN THIS DATA SET.
RfactorNum. reflection% reflectionSelection details
Rfree0.284 457 4 %RANDOM
Rwork0.199 ---
obs0.199 9882 89.4 %-
Displacement parametersBiso mean: 35.5 Å2
Refinement stepCycle: LAST / Resolution: 2.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2928 0 0 0 2928
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.57
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.9→3.03 Å / Rfactor Rfree error: 0.067 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.441 42 3.1 %
Rwork0.301 1031 -
obs--79.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

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