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- PDB-3caa: CLEAVED ANTICHYMOTRYPSIN A347R -

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Basic information

Entry
Database: PDB / ID: 3caa
TitleCLEAVED ANTICHYMOTRYPSIN A347R
Components(ANTICHYMOTRYPSIN) x 2
KeywordsSERPIN / SERINE PROTEASE INHIBITOR / ANTICHYMOTRYPSIN
Function / homology
Function and homology information


maintenance of gastrointestinal epithelium / regulation of lipid metabolic process / response to cytokine / platelet alpha granule lumen / acute-phase response / serine-type endopeptidase inhibitor activity / azurophil granule lumen / Platelet degranulation / : / secretory granule lumen ...maintenance of gastrointestinal epithelium / regulation of lipid metabolic process / response to cytokine / platelet alpha granule lumen / acute-phase response / serine-type endopeptidase inhibitor activity / azurophil granule lumen / Platelet degranulation / : / secretory granule lumen / blood microparticle / inflammatory response / Neutrophil degranulation / extracellular space / DNA binding / 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: 2.4 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 18, 1997Processing site: BNL
SupersessionFeb 25, 1998ID: 2CAA
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

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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)42,9712
Polymers42,9712
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-29 kcal/mol
Surface area15810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.120, 77.730, 79.490
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: 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
#2: Protein/peptide ANTICHYMOTRYPSIN / ACT


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 / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Compound detailsA: 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 BURIED IN A HYDROPHOBIC AREA.

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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: 2.75 Å3/Da / Density % sol: 55 %
Crystal growpH: 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
IDConc.Common nameCrystal-IDSol-ID
12 mg/mlprotein1drop
23.3 %mPEG50001drop
30.07 Mmagnesium acetate1drop
40.03 Msodium citrate1drop
510 %mPEG50001reservoir
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 QUANTUM / 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: 2.4→20 Å / Num. obs: 15560 / % possible obs: 83.7 % / Redundancy: 4.05 % / Rsym value: 0.101 / Net I/σ(I): 7.3
Reflection shellResolution: 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

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 2CAA

2caa
PDB Unreleased entry


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.
RfactorNum. reflection% reflectionSelection details
Rfree0.28 594 4 %RANDOM
Rwork0.19 ---
obs0.19 14515 78.46 %-
Displacement parametersBiso mean: 35.8 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2933 0 0 47 2980
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.022
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_deg2.11
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.92
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: 2.4→2.51 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.369 69 3 %
Rwork0.296 1595 -
obs--73.4 %
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
Refinement
*PLUS
Rfactor obs: 0.19 / Rfactor Rfree: 0.28 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.92

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