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- PDB-1hpt: THREE-DIMENSIONAL STRUCTURE OF A RECOMBINANT VARIANT OF HUMAN PAN... -

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Basic information

Entry
Database: PDB / ID: 1hpt
TitleTHREE-DIMENSIONAL STRUCTURE OF A RECOMBINANT VARIANT OF HUMAN PANCREATIC SECRETORY TRYPSIN INHIBITOR (KAZAL TYPE)
ComponentsPANCREATIC SECRETORY TRYPSIN INHIBITOR (KAZAL TYPE) VARIANT 3
KeywordsSERINE PROTEASE INHIBITOR
Function / homology
Function and homology information


negative regulation of nitric oxide mediated signal transduction / negative regulation of calcium ion import / regulation of acrosome reaction / regulation of store-operated calcium entry / Developmental Lineage of Pancreatic Acinar Cells / endopeptidase inhibitor activity / sperm capacitation / nitric oxide mediated signal transduction / serine-type endopeptidase inhibitor activity / extracellular exosome
Similarity search - Function
Proteinase inhibitor I1, Kazal-type, metazoa / Kazal serine protease inhibitors family signature. / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Serine protease inhibitor Kazal-type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsHecht, H.J. / Szardenings, M. / Collins, J. / Schomburg, D.
CitationJournal: J.Mol.Biol. / Year: 1992
Title: Three-dimensional structure of a recombinant variant of human pancreatic secretory trypsin inhibitor (Kazal type).
Authors: Hecht, H.J. / Szardenings, M. / Collins, J. / Schomburg, D.
History
DepositionMar 27, 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 1.3Jun 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 / 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 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PANCREATIC SECRETORY TRYPSIN INHIBITOR (KAZAL TYPE) VARIANT 3


Theoretical massNumber of molelcules
Total (without water)6,3471
Polymers6,3471
Non-polymers00
Water55831
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.150, 40.150, 33.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein PANCREATIC SECRETORY TRYPSIN INHIBITOR (KAZAL TYPE) VARIANT 3


Mass: 6347.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P00995
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.15 Å3/Da / Density % sol: 42.85 %
Crystal grow
*PLUS
pH: 8.3 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.0 Mammonium sulfate12
2100 mMTris-HCl12
310 mg/mlinhibitor11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.46 Å / Num. all: 2483 / Num. obs: 4612 / Num. measured all: 2200 / Rmerge(I) obs: 0.069

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.3→8 Å / Rfactor Rwork: 0.191 / Rfactor obs: 0.191 / σ(F): 2
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms440 0 0 31 471
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg2.7
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
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.191 / Num. reflection obs: 2200
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 14.2 Å2
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg
X-RAY DIFFRACTIONx_mcbond_it
LS refinement shell
*PLUS
Highest resolution: 4 Å / Lowest resolution: 10 Å / Rfactor all: 0.466

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