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- PDB-1att: CRYSTAL STRUCTURE OF CLEAVED BOVINE ANTITHROMBIN III AT 3.2 ANGST... -

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Basic information

Entry
Database: PDB / ID: 1att
TitleCRYSTAL STRUCTURE OF CLEAVED BOVINE ANTITHROMBIN III AT 3.2 ANGSTROMS RESOLUTION
ComponentsANTITHROMBIN III
KeywordsSERINE PROTEINASE INHIBITOR
Function / homology
Function and homology information


regulation of blood coagulation / serine-type endopeptidase inhibitor activity / blood coagulation / heparin binding / extracellular space
Similarity search - Function
Antithrombin-III, serpin domain / Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 ...Antithrombin-III, serpin domain / Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / 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
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 3.2 Å
AuthorsMourey, L. / Samama, J.P. / Delarue, M. / Moras, D.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: Crystal structure of cleaved bovine antithrombin III at 3.2 A resolution.
Authors: Mourey, L. / Samama, J.P. / Delarue, M. / Petitou, M. / Choay, J. / Moras, D.
#1: Journal: Biochimie / Year: 1990
Title: Antithrombin III: Structural and Functional Aspects
Authors: Mourey, L. / Samama, J.P. / Delarue, M. / Choay, J. / Lormeau, J.C. / Petitou, M. / Moras, D.
#2: Journal: Acta Crystallogr.,Sect.B / Year: 1990
Title: Crystal Structure of Bovine Antithrombin III
Authors: Delarue, M. / Samama, J.-P. / Mourey, L. / Moras, D.
#3: Journal: J.Mol.Biol. / Year: 1989
Title: Crystallization and Preliminary Crystallographic Data for Bovine Antithrombin III
Authors: Samama, J.P. / Delarue, M. / Mourey, L. / Choay, J. / Moras, D.
History
DepositionMar 29, 1993Processing site: BNL
Revision 1.0Jul 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ANTITHROMBIN III
B: ANTITHROMBIN III


Theoretical massNumber of molelcules
Total (without water)97,4112
Polymers97,4112
Non-polymers00
Water00
1
A: ANTITHROMBIN III


Theoretical massNumber of molelcules
Total (without water)48,7051
Polymers48,7051
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ANTITHROMBIN III


Theoretical massNumber of molelcules
Total (without water)48,7051
Polymers48,7051
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.300, 91.300, 383.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.07868, -0.99527, -0.057), (-0.04669, -0.06079, 0.99706), (-0.99581, -0.07578, -0.05125)
Vector: 170.4039, -258.8259, 371.64853)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN A WHEN APPLIED TO CHAIN B.

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Components

#1: Protein ANTITHROMBIN III


Mass: 48705.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P41361
Compound detailsTHE SPECIFIC N-TERMINAL EXTENSION OF ANTITHROMBIN III IS TIED TO THE MOLECULE BY TWO DISULFIDE ...THE SPECIFIC N-TERMINAL EXTENSION OF ANTITHROMBIN III IS TIED TO THE MOLECULE BY TWO DISULFIDE BRIDGES: CYS 9 - CYS 129 (MOST PROBABLY DISORDERED IN MOLECULE B) AND CYS 22 - CYS 96. AFTER THE CLEAVAGE SITE, THE C-TERMINAL DOMAIN IS LINKED TO THE MOLECULE BY THE DISULFIDE BOND CYS 248 - CYS 431.
Has protein modificationY
Sequence detailsSEQUENCE ANALYSIS OF DISSOLVED CRYSTALS SHOWED THAT CLEAVAGE HAD OCCURRED AT THE PEPTIDE BOND SER ...SEQUENCE ANALYSIS OF DISSOLVED CRYSTALS SHOWED THAT CLEAVAGE HAD OCCURRED AT THE PEPTIDE BOND SER 395 - LEU 396 (P1' - P2'). THE STRUCTURE DISPLAYS A TOPOLOGY SIMILAR TO THAT OF MODIFIED ALPHA-1-ANTITRYPSIN (LOEBERMANN ET AL., J. MOL. BIOL. 177, 531, 1984) WITH THE RESIDUES DELIMITING THE CLEAVAGE REGION WHICH ARE FOUND AT OPPOSITE ENDS OF THE MOLECULE. SEQUENCE ADVISORY NOTICE: THE SEQUENCE PRESENTED HERE IS OF THE BOVINE ANTITHROMBIN III AS REFERENCED BY H. MEJDOUB, M. LE RET, Y. BOULANGER, M. MAMAN, J. CHOAY, AND J. REINBOLT, J. PROTEIN CHEM., VOL. 10, PAGES 205-212, 1991.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.1 Å3/Da / Density % sol: 69.98 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
113 mg/mlprotein11
270 %satammonium sulphate12
330 mMpotassium12
41 mM12can be replaced with HgCl2, ZnCl2CdCl2
50.01 %(w/v)12NaN3

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 41 Å / Num. obs: 23436 / % possible obs: 84 % / Num. measured all: 61000 / Rmerge(I) obs: 0.091

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 3.2→8 Å /
RfactorNum. reflection
Rwork0.212 -
obs0.212 20702
Refinement stepCycle: LAST / Resolution: 3.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6640 0 0 0 6640
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg3.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.212 / Rfactor Rwork: 0.212
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d3.6
X-RAY DIFFRACTIONx_dihedral_angle_d26.09
X-RAY DIFFRACTIONx_dihedral_angle_deg1.51

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