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Basic information

Entry
Database: PDB / ID: 1oxg
TitleCrystal structure of a complex formed between organic solvent treated bovine alpha-chymotrypsin and its autocatalytically produced highly potent 14-residue peptide at 2.2 resolution
Components(Chymotrypsinogen A) x 2
KeywordsHYDROLASE / Autocatalysis / Organic solvent treatment / Inhibition
Function / homology
Function and homology information


chymotrypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / 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 / Mainly Beta
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSingh, N. / Jabeen, T. / Sharma, S. / Roy, I. / Gupta, M.N. / Bilgrami, S. / Singh, T.P.
CitationJournal: Febs J. / Year: 2005
Title: Detection of native peptides as potent inhibitors of enzymes. Crystal structure of the complex formed between treated bovine alpha-chymotrypsin and an autocatalytically produced fragment, IIe- ...Title: Detection of native peptides as potent inhibitors of enzymes. Crystal structure of the complex formed between treated bovine alpha-chymotrypsin and an autocatalytically produced fragment, IIe-Val-Asn-Gly-Glu-Glu-Ala-Val-Pro-Gly-Ser-Trp-Pro-Trp, at 2.2 angstroms resolution.
Authors: Singh, N. / Jabeen, T. / Sharma, S. / Roy, I. / Gupta, M.N. / Bilgrami, S. / Somvanshi, R.K. / Dey, S. / Perbandt, M. / Betzel, C. / Srinivasan, A. / Singh, T.P.
History
DepositionApr 2, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Oct 25, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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: Chymotrypsinogen A
B: Chymotrypsinogen A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8038
Polymers27,2272
Non-polymers5766
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-53 kcal/mol
Surface area10830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.187, 76.382, 105.098
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-1006-

SO4

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Components

#1: Protein Chymotrypsinogen A / Alpha Chymotrypsin


Mass: 25686.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Secretion: Pancreatic secretion / References: UniProt: P00766, chymotrypsin
#2: Protein/peptide Chymotrypsinogen A / Alpha Chymotrypsin


Mass: 1540.673 Da / Num. of mol.: 1 / Fragment: residues 1-14 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Secretion: Pancreatic secretion / References: UniProt: P00766, chymotrypsin
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O

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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: 2.07 Å3/Da / Density % sol: 40.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 0.2M Ammonium sulphate, 20mM Sodium acetate buffer, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.91 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 14, 2002 / Details: Mirror
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 11726 / Num. obs: 11673 / % possible obs: 98.7 % / Redundancy: 20.3 % / Biso Wilson estimate: 12.3 Å2 / Rsym value: 0.043 / Net I/σ(I): 18.4
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 23.9 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 564 / Rsym value: 0.093 / % possible all: 98.7

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ACB

1acb


Resolution: 2.2→19.69 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1842156.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.207 602 5.2 %RANDOM
Rwork0.192 ---
all0.207 11726 --
obs0.198 11673 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.6449 Å2 / ksol: 0.342322 e/Å3
Displacement parametersBiso mean: 21.6 Å2
Baniso -1Baniso -2Baniso -3
1--2.91 Å20 Å20 Å2
2--5.23 Å20 Å2
3----2.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1855 0 30 230 2115
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg2.3
X-RAY DIFFRACTIONc_dihedral_angle_d27.8
X-RAY DIFFRACTIONc_improper_angle_d1.88
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it2.112
X-RAY DIFFRACTIONc_scbond_it2.192
X-RAY DIFFRACTIONc_scangle_it2.862.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.239 84 4.4 %
Rwork0.186 1831 -
obs-280936 99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4SUL.PARAMSUL.TOP

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