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- PDB-1as4: CLEAVED ANTICHYMOTRYPSIN A349R -

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Basic information

Entry
Database: PDB / ID: 1as4
TitleCLEAVED ANTICHYMOTRYPSIN A349R
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 / collagen-containing extracellular matrix / blood microparticle / secretory granule lumen ...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 / collagen-containing extracellular matrix / blood microparticle / secretory granule lumen / 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
ACETATE ION / Alpha-1-antichymotrypsin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2.1 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: Nat.Struct.Biol. / Year: 1996
Title: Arginine Substitutions in the Hinge Region of Antichymotrypsin Affect Serpin Beta-Sheet Rearrangement
Authors: Lukacs, C.M. / Zhong, J.Q. / Plotnick, M.I. / Rubin, H. / Cooperman, B.S. / Christianson, D.W.
History
DepositionAug 12, 1997Processing site: BNL
Revision 1.0Feb 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_ref_seq_dif / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9303
Polymers42,8712
Non-polymers591
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-28 kcal/mol
Surface area15340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.700, 78.350, 79.230
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
Fragment: CHAIN A CONTAINS RESIDUES 20 - 358, CHAIN B CONTAINS RESIDUES 359 - 393
Mutation: A349R
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: 4259.000 Da / Num. of mol.: 1
Fragment: CHAIN A CONTAINS RESIDUES 20 - 358, CHAIN B CONTAINS RESIDUES 359 - 393
Mutation: A349R
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: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRESIDUE 349 IS AN ALA -> ARG MUTATION. THE ARGININE IS BURIED WITH AN ACETATE COUNTERION.

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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: 2.65 Å3/Da / Density % sol: 53 % / Description: COORDINATES FROM 2CAA USED FOR DIFF. FOUR.
Crystal growpH: 5.6
Details: 14% PEG MONOMETHYLETHER 5000, 0.2 M MAGNESIUM ACETATE 0.1 M SODIUM ACETATE PH 5.6 PROTEIN AT 3 MG/ML
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.8 mg/mlprotein1drop
25.4 %PEG50001drop
30.08 Mmagnesium acetate1drop
40.04 Msodium citrate1drop
514 %PEG50001reservoir
60.2 Mmagnesium acetate1reservoir
70.1 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 1, 1997 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 26288 / % possible obs: 98.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 24.76 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 8.9
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 2.6 / % possible all: 93.8
Reflection
*PLUS
Num. measured all: 95680

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
CCP4data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER / Resolution: 2.1→20 Å / Rfactor Rfree error: 0.0075 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1
Details: RESIDUES GLN 105 - GLU 109 ARE IN VERY POOR DENSITY, AND THEIR CONFORMATIONS SHOULD NOT BE CONSIDERED AS ACTUAL.
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1031 4 %RANDOM
Rwork0.198 ---
obs0.198 25225 94.8 %-
Displacement parametersBiso mean: 30.3 Å2
Refine analyzeLuzzati d res low obs: 20 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2948 0 3 57 3008
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.32
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.46
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.1
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: 2.1→2.2 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.291 101 3.6 %
Rwork0.267 2704 -
obs--86.41 %
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 Rfree: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.46
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.1

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