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- PDB-2gct: STRUCTURE OF GAMMA-CHYMOTRYPSIN IN THE RANGE PH 2.0 TO PH 10.5 SU... -

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Basic information

Entry
Database: PDB / ID: 2gct
TitleSTRUCTURE 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
Components
  • (GAMMA-CHYMOTRYPSIN ...) x 3
  • TETRAPEPTIDE ADDUCT
KeywordsHYDROLASE/PEPTIDE / HYDROLASE / SERINE PROTEINASE / HYDROLASE-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: 1.8 Å
AuthorsDixon, M.M. / Matthews, B.W.
Citation
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.
#1: Journal: Biochemistry / Year: 1989
Title: Is Gamma-Chymotrypsin a Tetrapeptide Acyl-Enzyme Adduct of Gamma-Chymotrypsin?
Authors: Dixon, M.M. / Matthews, B.W.
History
DepositionSep 4, 1990Processing site: BNL
Revision 1.0Oct 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 6, 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 1.4Mar 13, 2013Group: Other
Revision 1.5Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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
Remark 700SHEET THE SHEET PRESENTED AS *S1* ON SHEET RECORDS BELOW IS ACTUALLY A SIX-STRANDED BETA-BARREL. ...SHEET THE SHEET PRESENTED AS *S1* ON SHEET RECORDS BELOW IS ACTUALLY A SIX-STRANDED BETA-BARREL. THIS IS REPRESENTED BY A SEVEN-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET S2 OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. STRANDS 1, 2, 3, 4, 5, AND 7 OF SHEETS S2A AND S2B ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GAMMA-CHYMOTRYPSIN A
B: GAMMA-CHYMOTRYPSIN A
C: GAMMA-CHYMOTRYPSIN A
D: TETRAPEPTIDE ADDUCT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9466
Polymers25,7544
Non-polymers1922
Water2,360131
1
A: GAMMA-CHYMOTRYPSIN A
B: GAMMA-CHYMOTRYPSIN A
C: GAMMA-CHYMOTRYPSIN A
D: TETRAPEPTIDE ADDUCT
hetero molecules

A: GAMMA-CHYMOTRYPSIN A
B: GAMMA-CHYMOTRYPSIN A
C: GAMMA-CHYMOTRYPSIN A
D: TETRAPEPTIDE ADDUCT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,89212
Polymers51,5088
Non-polymers3844
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area18540 Å2
ΔGint-205 kcal/mol
Surface area17420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.800, 69.800, 98.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

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GAMMA-CHYMOTRYPSIN ... , 3 types, 3 molecules ABC

#1: Protein/peptide GAMMA-CHYMOTRYPSIN A


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


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 A


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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Protein/peptide , 1 types, 1 molecules D

#4: Protein/peptide TETRAPEPTIDE ADDUCT


Mass: 491.538 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

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Non-polymers , 2 types, 133 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHE GAMMA CHYMOTRYPSIN MOLECULE IS COMPRISED OF THREE POLYPEPTIDE CHAINS WHICH ARE DERIVED FROM THE ...THE GAMMA CHYMOTRYPSIN MOLECULE IS COMPRISED OF THREE POLYPEPTIDE CHAINS WHICH ARE DERIVED FROM THE ZYMOGEN OF THIS ENZYME BY EXCISION OF RESIDUES 14-15 AND 147-148. TO ASSIGN SEPARATE CHAIN IDENTIFIERS TO THE THREE CHAINS WOULD OBSCURE THIS RELATIONSHIP AND SO THIS WAS NOT DONE. CHAIN TERMINATOR RECORDS WERE INSERTED AFTER RESIDUES 146 AND 245 TO INDICATE EXPLICIT TERMINI AND THE SPECIAL CODE EXC WAS USED IN THE SEQRES RECORDS TO DENOTE THE EXCISIONS. RESIDUES 11 THROUGH 13 AND 149 THROUGH 150 ARE NOT VISIBLE IN THE ELECTRON DENSITY MAP AND SO ARE OMITTED. IN THE ABSENCE OF RESIDUE 13 THE TER RECORD WHICH WOULD HAVE APPEARED AFTER RESIDUE 13 IS ALSO OMITTED. RESIDUES B 500 - B 504 ARE A TETRAPEPTIDE BOUND IN THE ACTIVE SITE, COVALENTLY LINKED TO OG OF SER 195 AS AN ACYL ADDUCT. IT IS, PRESUMABLY, AN AUTOLYTIC CLEAVAGE PRODUCT. THE EXACT IDENTITY OF THE RESIDUES IS UNCERTAIN AS THE SIDE CHAINS SEEM TO BE DISORDERED. THE ATOM IDENTIFIED AS C UNK B 500 IS ACTUALLY THE CARBONYL CARBON OF AN UNIDENTIFIED AMINO ACID NOT VISIBLE IN THE ELECTRON DENSITY MAP.

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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: 2.33 Å3/Da / Density % sol: 47.19 %
Crystal growpH: 2 / Details: pH 2.0
Crystal grow
*PLUS
pH: 7 / Method: batch method
Components of the solutions
*PLUS
Conc.: 50 %sat / Common name: ammonium sulfate

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Data collection

DiffractionMean temperature: 285 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54
DetectorType: KODAK / Detector: FILM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 10 Å / Num. obs: 13431 / % possible obs: 63.2 % / Num. measured all: 17029 / Rmerge(I) obs: 0.068

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Processing

Software
NameClassification
TNTrefinement
OSCTSTdata reduction
AGROVATA/ROTAVATEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→10 Å / Rfactor Rwork: 0.169
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1766 0 10 131 1907
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_bond_d0.019
X-RAY DIFFRACTIONt_angle_deg3.1
X-RAY DIFFRACTIONt_dihedral_angle_d18.10
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle0
X-RAY DIFFRACTIONt_trig_c_planes0.02
X-RAY DIFFRACTIONt_gen_planes0.021
X-RAY DIFFRACTIONt_it0
X-RAY DIFFRACTIONt_nbd
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg18.1
X-RAY DIFFRACTIONt_plane_restr0.021

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