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- PDB-1ciq: COMPLEX OF TWO FRAGMENTS OF CI2, RESIDUES 1-40 AND 41-64 -

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Basic information

Entry
Database: PDB / ID: 1ciq
TitleCOMPLEX OF TWO FRAGMENTS OF CI2, RESIDUES 1-40 AND 41-64
Components(CHYMOTRYPSIN INHIBITOR 2) x 2
KeywordsSERINE PROTEASE INHIBITOR / CLEAVED INHIBITOR
Function / homologyProteinase inhibitor I13, potato inhibitor I / Proteinase inhibitor I13, potato inhibitor I superfamily / Potato inhibitor I family / Potato inhibitor I family signature. / serine-type endopeptidase inhibitor activity / response to wounding / Subtilisin-chymotrypsin inhibitor-2A
Function and homology information
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsBuckle, A.M. / Fersht, A.R.
Citation
Journal: Structure Fold.Des. / Year: 1996
Title: Towards the complete structural characterization of a protein folding pathway: the structures of the denatured, transition and native states for the association/folding of two complementary ...Title: Towards the complete structural characterization of a protein folding pathway: the structures of the denatured, transition and native states for the association/folding of two complementary fragments of cleaved chymotrypsin inhibitor 2. Direct evidence for a nucleation-condensation mechanism
Authors: Neira, J.L. / Davis, B. / Ladurner, A.G. / Buckle, A.M. / Gay Gde, P. / Fersht, A.R.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: The Structure of the Transition State for the Association of Two Fragments of the Barley Chymotrypsin Inhibitor-2 to Generate Native-Like Protein: Implications for Mechanisms of Protein Folding
Authors: De Prat Gay, G. / Ruiz-Sanz, J. / Davis, B. / Fersht, A.R.
#2: Journal: Biochemistry / Year: 1994
Title: Generation of a Family of Protein Fragments for Structure-Folding Studies. 1. Folding Complementation of Two Fragments of Chymotrypsin Inhibitor-2 Formed by Cleavage at its Unique Methionine Residue
Authors: De Prat Gay, G. / Fersht, A.R.
History
DepositionOct 2, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHYMOTRYPSIN INHIBITOR 2
B: CHYMOTRYPSIN INHIBITOR 2


Theoretical massNumber of molelcules
Total (without water)7,3322
Polymers7,3322
Non-polymers00
Water88349
1
A: CHYMOTRYPSIN INHIBITOR 2
B: CHYMOTRYPSIN INHIBITOR 2
x 6


Theoretical massNumber of molelcules
Total (without water)43,99012
Polymers43,99012
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
MethodPQS
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-13 kcal/mol
Surface area4110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.170, 69.170, 53.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622

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Components

#1: Protein/peptide CHYMOTRYPSIN INHIBITOR 2 / CI2


Mass: 4454.312 Da / Num. of mol.: 1 / Fragment: RESIDUES 1 - 40, 41 - 64
Source method: isolated from a genetically manipulated source
Details: CLEAVED BETWEEN 40 AND 41 / Source: (gene. exp.) Hordeum vulgare (barley) / Strain: HIPROLY / Plasmid: PTZ18U / Production host: Escherichia coli (E. coli) / References: UniProt: P01053
#2: Protein/peptide CHYMOTRYPSIN INHIBITOR 2 / CI2


Mass: 2877.325 Da / Num. of mol.: 1 / Fragment: RESIDUES 1 - 40, 41 - 64
Source method: isolated from a genetically manipulated source
Details: CLEAVED BETWEEN 40 AND 41 / Source: (gene. exp.) Hordeum vulgare (barley) / Strain: HIPROLY / Plasmid: PTZ18U / Production host: Escherichia coli (E. coli) / References: UniProt: P01053
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE TWO FRAGMENTS (1 - 40 AND 41 - 64) WERE PRODUCED BY THE CLEAVAGE OF THE MET 40 - GLU 41 PEPTIDE ...THE TWO FRAGMENTS (1 - 40 AND 41 - 64) WERE PRODUCED BY THE CLEAVAGE OF THE MET 40 - GLU 41 PEPTIDE BOND BY CYANOGEN BROMIDE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.53 %
Crystal grow
*PLUS
Temperature: 23 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Details: drop solution is mixed 1:1 by volume with reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
122 mg/mlreconstituted fragment complex1drop
240 %satammonium sulfate1reservoir
350 mMTris-HCl1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 14, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→26.96 Å / Num. obs: 4179 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 5.3 % / Rmerge(I) obs: 0.05
Reflection
*PLUS
Num. measured all: 23355 / Rmerge(I) obs: 0.005
Reflection shell
*PLUS
% possible obs: 97.1 % / Rmerge(I) obs: 0.106

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Processing

Software
NameClassification
PROLSQrefinement
MOSFLMdata reduction
CCP4data reduction
RefinementResolution: 2.2→7 Å / σ(F): 0 /
RfactorNum. reflection% reflection
obs0.18 4024 99.8 %
Displacement parametersBiso mean: 20.1 Å2
Refinement stepCycle: LAST / Resolution: 2.2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms486 0 0 49 535
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.017
X-RAY DIFFRACTIONp_angle_d0.040.055
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.060.059
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.51.131
X-RAY DIFFRACTIONp_mcangle_it21.858
X-RAY DIFFRACTIONp_scbond_it22.92
X-RAY DIFFRACTIONp_scangle_it34.59
X-RAY DIFFRACTIONp_plane_restr0.020.013
X-RAY DIFFRACTIONp_chiral_restr0.120.128
X-RAY DIFFRACTIONp_singtor_nbd0.50.202
X-RAY DIFFRACTIONp_multtor_nbd0.50.228
X-RAY DIFFRACTIONp_xhyhbond_nbd0.50
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor32.284
X-RAY DIFFRACTIONp_staggered_tor2021.5
X-RAY DIFFRACTIONp_orthonormal_tor158.374
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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