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- PDB-1hja: LYS 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEX... -

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Basic information

Entry
Database: PDB / ID: 1hja
TitleLYS 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEXED WITH ALPHA-CHYMOTRYPSIN
Components
  • (ALPHA-CHYMOTRYPSIN) x 3
  • OVOMUCOID INHIBITOR
KeywordsCOMPLEX (HYDROLASE/INHIBITOR) / COMPLEX (HYDROLASE-INHIBITOR) / ALPHA-CHYMOTRYPSIN / PROTEIN INHIBITOR / COMPLEX (HYDROLASE-INHIBITOR) complex
Function / homology
Function and homology information


chymotrypsin / molecular function inhibitor activity / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / serine-type endopeptidase activity / proteolysis / extracellular region
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 / Serine proteases, trypsin family, histidine active site ...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 / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chymotrypsinogen A / Ovomucoid
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Meleagris gallopavo (turkey)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDing, J.-H. / James, M.N.G.
Citation
Journal: To be Published
Title: Crystal Structure of Lys18 Variant of Turkey Ovomucoid Inhibitor Third Domain Complexed with Alpha-Chymotrypsin at 2.3 A
Authors: Ding, J. / Qasim, M.A. / Laskowski Junior, M. / James, M.N.G.
#1: Journal: J.Mol.Biol. / Year: 1987
Title: Crystal and Molecular Structures of the Complex of Alpha-Chymotrypsin with its Inhibitor Turkey Ovomucoid Third Domain at 1.8 A Resolution
Authors: Fujinaga, M. / Sielecki, A.R. / Read, R.J. / Ardelt, W. / Laskowski Junior, M. / James, M.N.
History
DepositionJul 9, 1997Processing site: BNL
Revision 1.0Jan 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 1, 2016Group: Database references
Revision 1.4Apr 4, 2018Group: Data collection / Other / Category: diffrn_source / pdbx_database_status
Item: _diffrn_source.type / _pdbx_database_status.process_site
Revision 1.5Aug 9, 2023Group: Database references / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALPHA-CHYMOTRYPSIN
B: ALPHA-CHYMOTRYPSIN
C: ALPHA-CHYMOTRYPSIN
I: OVOMUCOID INHIBITOR


Theoretical massNumber of molelcules
Total (without water)30,8644
Polymers30,8644
Non-polymers00
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8930 Å2
ΔGint-66 kcal/mol
Surface area11600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.470, 103.470, 47.120
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein/peptide ALPHA-CHYMOTRYPSIN


Mass: 1253.511 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: COMMERCIAL PRODUCT OF WORTHINGTON BIOCHEMICAL CORPORATION
Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00766, chymotrypsin
#2: Protein ALPHA-CHYMOTRYPSIN


Mass: 13934.556 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle)
Description: COMMERCIAL PRODUCT OF WORTHINGTON BIOCHEMICAL CORPORATION
Plasmid: PEZZ318.TKY / Production host: Escherichia coli (E. coli) / References: UniProt: P00766, chymotrypsin
#3: Protein ALPHA-CHYMOTRYPSIN


Mass: 10074.495 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle)
Description: COMMERCIAL PRODUCT OF WORTHINGTON BIOCHEMICAL CORPORATION
Plasmid: PEZZ318.TKY / Production host: Escherichia coli (E. coli) / References: UniProt: P00766, chymotrypsin
#4: Protein OVOMUCOID INHIBITOR / LYS18-OMTKY3


Mass: 5601.311 Da / Num. of mol.: 1
Fragment: THIRD DOMAIN, DELETION OF FIRST 5 RESIDUES FROM N-TERMINUS
Mutation: DEL(1-5), L18K
Source method: isolated from a genetically manipulated source
Details: TURKEY OVOMUCOID INHIBITOR / Source: (gene. exp.) Meleagris gallopavo (turkey) / Plasmid: PEZZ318.TKY / Production host: Escherichia coli (E. coli) / References: UniProt: P68390
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 47.84 %
Description: ALPHA-CHYMOTRYPSIN (E.C.3.4.21.1) COMPLEX WITH TURKEY OVOMUCOID THIRD DOMAIN
Crystal growpH: 6 / Details: 0.1 M KH2PO4/K2HPO4 PH=6.0 10% PEG6000

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Nov 4, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→10 Å / Num. obs: 11136 / % possible obs: 86.9 % / Observed criterion σ(I): 1 / Redundancy: 8.7 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 5.89
Reflection shellResolution: 2.3→2.4 Å / % possible all: 69.27

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Processing

Software
NameVersionClassification
XENGENdata collection
XENGENdata reduction
X-PLOR3.843model building
X-PLOR3.843refinement
XENGENdata scaling
X-PLOR3.843phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CHO

1cho


Resolution: 2.3→10 Å / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.246 -10 %
Rwork0.193 --
obs0.193 11136 86.9 %
Displacement parametersBiso mean: 14.55 Å2
Refine analyzeLuzzati sigma a obs: 0.36 Å
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2138 0 0 99 2237
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.536
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.43
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.331
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: 2.3→2.4 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.31 -9.6 %
Rwork0.2707 997 -
obs--69.27 %

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