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- PDB-1ab9: CRYSTAL STRUCTURE OF BOVINE GAMMA-CHYMOTRYPSIN -

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Basic information

Entry
Database: PDB / ID: 1ab9
TitleCRYSTAL STRUCTURE OF BOVINE GAMMA-CHYMOTRYPSIN
Components
  • (GAMMA-CHYMOTRYPSIN) x 3
  • PENTAPEPTIDE (TPGVY)
KeywordsCOMPLEX (SERINE PROTEASE/PEPTIDE) / HYDROLASE / SERINE PROTEASE / DIGESTION / PANCREAS / ZYMOGEN / COMPLEX (SERINE PROTEASE-PEPTIDE) / COMPLEX (SERINE PROTEASE-PEPTIDE) complex
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 / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSugio, S. / Kashima, A. / Inoue, Y. / Maeda, I. / Nose, T. / Shimohigashi, Y.
Citation
Journal: Eur.J.Biochem. / Year: 1998
Title: X-ray crystal structure of a dipeptide-chymotrypsin complex in an inhibitory interaction.
Authors: Kashima, A. / Inoue, Y. / Sugio, S. / Maeda, I. / Nose, T. / Shimohigashi, Y.
#1: Journal: Biochemistry / Year: 1991
Title: Gamma-Chymotrypsin is a Complex of Alpha-Chymotrypsin with its Own Autolysis Products
Authors: Harel, M. / Su, C.T. / Frolow, F. / Silman, I. / Sussman, J.L.
#2: Journal: Int.J.Biol.Macromol. / Year: 1991
Title: Structure of Gamma-Chymotrypsin in the Range Ph 2.0 To Ph 10.5 Suggests that Gamma-Chymotrypsin is a Covalent Acyl-Enzyme Adduct at Low Ph
Authors: Dixon, M.M. / Brennan, R.G. / Matthews, B.W.
#3: Journal: Biochemistry / Year: 1989
Title: Is Gamma-Chymotrypsin a Tetrapeptide Acyl-Enzyme Adduct of Alpha-Chymotrypsin?
Authors: Dixon, M.M. / Matthews, B.W.
History
DepositionFeb 5, 1997Processing site: BNL
Revision 1.0Aug 20, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Mar 13, 2013Group: Other
Revision 1.5Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
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_conn.pdbx_leaving_atom_flag / _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: GAMMA-CHYMOTRYPSIN
B: GAMMA-CHYMOTRYPSIN
C: GAMMA-CHYMOTRYPSIN
D: PENTAPEPTIDE (TPGVY)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8945
Polymers25,7984
Non-polymers961
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7950 Å2
ΔGint-76 kcal/mol
Surface area10230 Å2
MethodPISA
2
A: GAMMA-CHYMOTRYPSIN
B: GAMMA-CHYMOTRYPSIN
C: GAMMA-CHYMOTRYPSIN
D: PENTAPEPTIDE (TPGVY)
hetero molecules

A: GAMMA-CHYMOTRYPSIN
B: GAMMA-CHYMOTRYPSIN
C: GAMMA-CHYMOTRYPSIN
D: PENTAPEPTIDE (TPGVY)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,78810
Polymers51,5968
Non-polymers1922
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area18470 Å2
ΔGint-175 kcal/mol
Surface area17880 Å2
MethodPISA
3
A: GAMMA-CHYMOTRYPSIN

A: GAMMA-CHYMOTRYPSIN

B: GAMMA-CHYMOTRYPSIN
C: GAMMA-CHYMOTRYPSIN
D: PENTAPEPTIDE (TPGVY)
hetero molecules

B: GAMMA-CHYMOTRYPSIN
C: GAMMA-CHYMOTRYPSIN
D: PENTAPEPTIDE (TPGVY)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,78810
Polymers51,5968
Non-polymers1922
Water1448
TypeNameSymmetry operationNumber
crystal symmetry operation5_545-x+1/2,y-1/2,-z+1/21
crystal symmetry operation6_555x+1/2,-y+1/2,-z+1/21
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area17130 Å2
ΔGint-160 kcal/mol
Surface area19230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.520, 69.520, 97.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11B-607-

HOH

21B-608-

HOH

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Components

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Protein/peptide , 2 types, 2 molecules AD

#1: Protein/peptide GAMMA-CHYMOTRYPSIN


Mass: 1253.511 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00766, chymotrypsin
#4: Protein/peptide PENTAPEPTIDE (TPGVY)


Mass: 535.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

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Protein , 2 types, 2 molecules BC

#2: Protein GAMMA-CHYMOTRYPSIN


Mass: 13934.556 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00766, chymotrypsin
#3: Protein GAMMA-CHYMOTRYPSIN


Mass: 10074.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00766, chymotrypsin

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Non-polymers , 2 types, 128 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHE BOUND PENTAPEPTIDE (THR D 300 TO TYR D 304) HAVE TWO DIFFERENT CONFORMATIONS. THE OCCUPANCIES ...THE BOUND PENTAPEPTIDE (THR D 300 TO TYR D 304) HAVE TWO DIFFERENT CONFORMATIONS. THE OCCUPANCIES OF ALL THE ATOMS IN THE PEPTIDE WERE SET TO 0.5.

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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: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 5.6
Details: ALPHA-CHYMOTRYPSIN WAS DISSOLVED IN POTASSIUM BORATE (PH8.6) AND WAS INCUBATED AT 310K FOR 6 HOURS. SOLID AMMONIUM SULFATE WAS ADDED TO THE SOLUTION, AND THE PRECIPITATE FORMED WAS RECOVERED ...Details: ALPHA-CHYMOTRYPSIN WAS DISSOLVED IN POTASSIUM BORATE (PH8.6) AND WAS INCUBATED AT 310K FOR 6 HOURS. SOLID AMMONIUM SULFATE WAS ADDED TO THE SOLUTION, AND THE PRECIPITATE FORMED WAS RECOVERED AND RE-DISSOLVED WITH WATER. CRYSTALLIZATION WAS DONE WITH A SITTING-DROP VAPOR-DIFFUSION PROCEDURE, IN WHICH PROTEIN SOLUTION (15MG/ML) CONTAINING 10MM CACODYLATE, 0.75% SATURATED ACETYLTRIMETHYL AMMONIUM AND 45% SATURATED AMMONIUM SULFATE WAS EQUILIBRATED AGAINST 65% SATURATED AMMONIUM SULFATE AT 293K., pH 5.6, vapor diffusion - sitting drop
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlchymotrypsin1drop
210 mMsodium cacodylate1drop
30.75 %satcetyltrimethylammonium bromide1drop
445 %satammonium sulfate1drop
565 %satammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 292 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 24, 1995 / Details: YALE MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→69.5 Å / Num. obs: 31740 / % possible obs: 97.8 % / Observed criterion σ(I): 1 / Redundancy: 10.3 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 15.1
Reflection shellResolution: 1.6→1.65 Å / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 3.1 / % possible all: 94.7
Reflection
*PLUS
Num. measured all: 332021
Reflection shell
*PLUS
% possible obs: 94.7 %

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Processing

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

1gct


Resolution: 1.6→5 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: POSTERIORI / σ(F): 2
Details: THE FOLLOWING WEIGHTING SCHEME WAS USED: 1/(SIGMAF)**2 SIDE CHAINS OF VAL B 53 AND GLN C 239 HAVE ALTERNATE CONFORMATIONS. THE OCCUPANCIES OF THE CORRESPONDING ATOMS WERE SET TO 0.5.
RfactorNum. reflection% reflectionSelection details
Rfree0.19 2496 8 %RANDOM
Rwork0.191 ---
obs0.191 30329 97.3 %-
Displacement parametersBiso mean: 21.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 1.6→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1821 0 5 127 1953
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.42
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.26
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shellResolution: 1.6→1.66 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.263 243 8 %
Rwork0.285 2630 -
obs--93.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM.PARTOPOL.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.26
LS refinement shell
*PLUS
Rfactor obs: 0.285

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