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- PDB-1nag: CREVICE-FORMING MUTANTS IN THE RIGID CORE OF BOVINE PANCREATIC TR... -

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Basic information

Entry
Database: PDB / ID: 1nag
TitleCREVICE-FORMING MUTANTS IN THE RIGID CORE OF BOVINE PANCREATIC TRYPSIN INHIBITOR: CRYSTAL STRUCTURES OF F22A, Y23A, N43G, AND F45A
ComponentsBOVINE PANCREATIC TRYPSIN INHIBITOR
KeywordsSERINE PROTEASE INHIBITOR
Function / homology
Function and homology information


trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / serine protease inhibitor complex / serine-type endopeptidase inhibitor activity ...trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / serine protease inhibitor complex / serine-type endopeptidase inhibitor activity / protease binding / calcium ion binding / extracellular space
Similarity search - Function
: / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily ...: / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
PHOSPHATE ION / Pancreatic trypsin inhibitor
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsDanishefsky, A.T. / Wlodawer, A. / Kim, K.-S. / Tao, F. / Woodward, C.
Citation
Journal: Protein Sci. / Year: 1993
Title: Crevice-forming mutants in the rigid core of bovine pancreatic trypsin inhibitor: crystal structures of F22A, Y23A, N43G, and F45A.
Authors: Danishefsky, A.T. / Housset, D. / Kim, K.S. / Tao, F. / Fuchs, J. / Woodward, C. / Wlodawer, A.
#1: Journal: Protein Sci. / Year: 1993
Title: Crevice-Forming Mutants of Bovine Pancreatic Trypsin Inhibitor: Stability Changes and New Hydrophobic Surface
Authors: Tao, K.-S.Kim.F. / Fuchs, J. / Danishefsky, A.T. / Housset, D. / Wlodawer, A. / Woodward, C.
#2: Journal: J.Mol.Biol. / Year: 1991
Title: Crystal Structure of a Y35G Mutant of Bovine Pancreatic Trypsin Inhibitor
Authors: Housset, D. / Kim, K.-S. / Fuchs, J. / Woodward, C. / Wlodawer, A.
#3: Journal: Protein Eng. / Year: 1990
Title: Structural Effects Induced by Removal of a Disulfide-Bridge. The X-Ray Structure of the C30A(Slash)C51A Mutant of Basic Pancreatic Trypsin Inhibitor at 1.6 Angstroms
Authors: Eigenbrot, C. / Randal, M. / Kossiakoff, A.A.
#4: Journal: Biochemistry / Year: 1990
Title: X-Ray Crystal Structure of the Protease Inhibitor Domain of Alzheimer'S Amyloid Beta-Protein Precursor
Authors: Hynes, T.R. / Randal, M. / Kennedy, L.A. / Eigenbrot, C. / Kossiakoff, A.A.
#5: Journal: J.Mol.Biol. / Year: 1987
Title: Structure of Form III Crystals of Bovine Pancreatic Trypsin Inhibitor
Authors: Wlodawer, A. / Nachman, J. / Gilliland, G.L. / Gallagher, W. / Woodward, C.
#6: Journal: J.Mol.Biol. / Year: 1987
Title: Comparison of Two Highly Refined Structures of Bovine Pancreatic Trypsin Inhibitor
Authors: Wlodawer, A. / Deisenhofer, J. / Huber, R.
#7: Journal: J.Mol.Biol. / Year: 1984
Title: Structure of Bovine Pancreatic Trypsin Inhibitor. Results of Joint Neutron and X-Ray Refinement of Crystal Form II
Authors: Wlodawer, A. / Walter, J. / Huber, R. / Sjolin, L.
#8: Journal: J.Mol.Biol. / Year: 1983
Title: Pancreatic Trypsin Inhibitor. A New Crystal Form and its Analysis
Authors: Walter, J. / Huber, R.
History
DepositionAug 18, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BOVINE PANCREATIC TRYPSIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5652
Polymers6,4711
Non-polymers951
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.720, 37.980, 23.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-236-

HOH

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Components

#1: Protein BOVINE PANCREATIC TRYPSIN INHIBITOR


Mass: 6470.517 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P00974
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.73 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 9 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein solution1drop
20.6 Mpotassium phosphate1drop
31.2-1.3 Mpotassium phosphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 10 Å / Num. obs: 4421 / % possible obs: 98 % / Rmerge(I) obs: 0.058

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.9→10 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.163 -
obs0.163 4266
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms440 0 5 64 509
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.013
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_deg
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_it0.9961.5
X-RAY DIFFRACTIONx_mcangle_it1.4422
X-RAY DIFFRACTIONx_scbond_it3.2093
X-RAY DIFFRACTIONx_scangle_it4.9394
Refinement
*PLUS
Rfactor obs: 0.163
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_angle_d0.040.036
X-RAY DIFFRACTIONx_planar_d0.050.037
X-RAY DIFFRACTIONx_plane_restr0.020.011
X-RAY DIFFRACTIONx_chiral_restr0.150.14

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