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- PDB-1afq: CRYSTAL STRUCTURE OF BOVINE GAMMA-CHYMOTRYPSIN COMPLEXED WITH A S... -

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Basic information

Entry
Database: PDB / ID: 1afq
TitleCRYSTAL STRUCTURE OF BOVINE GAMMA-CHYMOTRYPSIN COMPLEXED WITH A SYNTHETIC INHIBITOR
Components(BOVINE GAMMA- ...) x 3
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR 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 / 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 ...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 / Mainly Beta
Similarity search - Domain/homology
D-LEUCYL-L-PHENYLALANYL-P-FLUOROBENZYLAMIDE / D-leucyl-N-(4-fluorobenzyl)-L-phenylalaninamide / Chymotrypsinogen A
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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
DepositionMar 12, 1997Processing site: BNL
Revision 1.0Sep 17, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Aug 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BOVINE GAMMA-CHYMOTRYPSIN
B: BOVINE GAMMA-CHYMOTRYPSIN
C: BOVINE GAMMA-CHYMOTRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0586
Polymers25,1913
Non-polymers8673
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.840, 69.840, 97.360
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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BOVINE GAMMA- ... , 3 types, 3 molecules ABC

#1: Protein/peptide BOVINE GAMMA-CHYMOTRYPSIN


Mass: 1253.511 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: PANCREAS / References: UniProt: P00766, chymotrypsin
#2: Protein BOVINE GAMMA-CHYMOTRYPSIN


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


Mass: 10003.417 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: PANCREAS / References: UniProt: P00766, chymotrypsin

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Non-polymers , 3 types, 130 molecules

#4: Chemical ChemComp-0FG / D-leucyl-N-(4-fluorobenzyl)-L-phenylalaninamide


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 385.475 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H28FN3O2 / Details: AN INHIBITOR FOR CHYMOTRYPSIN / References: D-LEUCYL-L-PHENYLALANYL-P-FLUOROBENZYLAMIDE
#5: Chemical ChemComp-SO4 / SULFATE ION


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


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

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Details

Has protein modificationY
Nonpolymer detailsTHERE ARE TWO INHIBITOR MOLECULES IN AN ASYMMETRIC UNIT. ONE (CHAIN C) IS BOUND TO SUBSTRATE ...THERE ARE TWO INHIBITOR MOLECULES IN AN ASYMMETRIC UNIT. ONE (CHAIN C) IS BOUND TO SUBSTRATE BINDING SITE, WHILE THE OTHER (CHAIN B) IS LOCATED AT THE INTERFACE OF THE PROTEIN MOLECULES APART FROM THE CATALYTIC SITE.

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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: 46.18 %
Crystal growTemperature: 293 K / pH: 7.5
Details: GAMMA-CHYMOTRYPSIN CRYSTALS WERE SOAKED INTO A SOLUTION CONTAINING SATURATED INHIBITOR, 65% SATURATED AMMONIUM SULFATE AND 100 MM HEPES BUFFER (PH7.5) AT 293K FOR A MONTH.
Crystal grow
*PLUS
pH: 5.6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlchymotrypsin1drop
210.5 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 / Detector: IMAGE PLATE / Date: Nov 10, 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: 1.8→97.4 Å / Num. obs: 22647 / % possible obs: 98.1 % / Observed criterion σ(I): 1 / Redundancy: 9.5 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 13.5
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.128 / Mean I/σ(I) obs: 4.09 / % possible all: 95.6
Reflection
*PLUS
Num. measured all: 215467
Reflection shell
*PLUS
% possible obs: 94.6 % / Rmerge(I) obs: 0.143 / Mean I/σ(I) obs: 4.1

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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 1AB9

1ab9


Resolution: 1.8→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
RfactorNum. reflection% reflectionSelection details
Rfree0.182 1683 7.9 %RANDOM
Rwork0.181 ---
obs0.181 21268 97.6 %-
Displacement parametersBiso mean: 22.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 1.8→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1745 0 61 127 1933
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.47
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_d1.25
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: 1.8→1.86 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.204 159 7.5 %
Rwork0.245 1841 -
obs--93.9 %
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
Biso mean: 17.8 Å2
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_deg1.25
LS refinement shell
*PLUS
Rfactor obs: 0.245

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