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- PDB-1gmd: X-ray crystal structure of gamma-chymotrypsin in hexane -

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Basic information

Entry
Database: PDB / ID: 1gmd
TitleX-ray crystal structure of gamma-chymotrypsin in hexane
Components
  • (GAMMA-CHYMOTRYPSIN ...) x 3
  • PRO GLY ALA TYR ASP PEPTIDE
KeywordsHYDROLASE / SERINE PROTEASE
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
HEXANE / Chymotrypsinogen A
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsYennawar, N.H. / Yennawar, H.P. / Banerjee, S. / Farber, G.K.
CitationJournal: Biochemistry / Year: 1994
Title: X-ray crystal structure of gamma-chymotrypsin in hexane.
Authors: Yennawar, N.H. / Yennawar, H.P. / Farber, G.K.
History
DepositionAug 20, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 24, 2013Group: Derived calculations
Revision 1.4Jun 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
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700SHEET THE SHEETS PRESENTED AS *S1* AND *S2* ON SHEET RECORDS BELOW ARE ACTUALLY SIX-STRANDED BETA ...SHEET THE SHEETS PRESENTED AS *S1* AND *S2* ON SHEET RECORDS BELOW ARE ACTUALLY SIX-STRANDED BETA BARRELS. THIS IS REPRESENTED BY SEVEN-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: GAMMA-CHYMOTRYPSIN A
F: GAMMA-CHYMOTRYPSIN A
G: GAMMA-CHYMOTRYPSIN A
B: PRO GLY ALA TYR ASP PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,38711
Polymers25,7844
Non-polymers6037
Water2,342130
1
E: GAMMA-CHYMOTRYPSIN A
F: GAMMA-CHYMOTRYPSIN A
G: GAMMA-CHYMOTRYPSIN A
B: PRO GLY ALA TYR ASP PEPTIDE
hetero molecules

E: GAMMA-CHYMOTRYPSIN A
F: GAMMA-CHYMOTRYPSIN A
G: GAMMA-CHYMOTRYPSIN A
B: PRO GLY ALA TYR ASP PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,77522
Polymers51,5688
Non-polymers1,20614
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
Unit cell
Length a, b, c (Å)69.340, 69.320, 97.510
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 EFG

#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 (domestic 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 (domestic 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 (domestic cattle) / References: UniProt: P00766, chymotrypsin

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Protein/peptide , 1 types, 1 molecules B

#4: Protein/peptide PRO GLY ALA TYR ASP PEPTIDE


Mass: 521.521 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)

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Non-polymers , 2 types, 137 molecules

#5: Chemical
ChemComp-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsRESIDUES 500 - 505 ARE A PENTAPEPTIDE IN THE ACTIVE SITE AS A TETRAHEDRAL INTERMEDIATE. C OF ...RESIDUES 500 - 505 ARE A PENTAPEPTIDE IN THE ACTIVE SITE AS A TETRAHEDRAL INTERMEDIATE. C OF RESIDUE TYR 504 IS TETRAHEDRAL AND IS COVALENTLY LINKED TO SER 195 OG AND N OF ASP 505. THE CARBOXY TERMINUS OF ASP 505 WAS NOT CLEAR IN THE ELECTRON DENSITY MAP AND HAS NOT BEEN MODELLED.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.85 %
Crystal grow
*PLUS
pH: 5.6 / Method: batch method
Details: referred to 'Stoddard, B. L.', (1990) Biochemistry, 29, 4871-4879
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlchymotrypsin11
210 mMsodium cacodylate11
30.75 %satcetyltrimethylammonium bromide11
445 %satammonium sulfate11
565 %satammonium sulphate12

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.2 Å
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. obs: 7606 / Observed criterion σ(I): 2 / Num. measured all: 13982 / Rmerge(I) obs: 0.092

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Processing

SoftwareName: X-PLOR / Version: 1GMD / Classification: refinement
RefinementRfactor Rwork: 0.176 / Rfactor obs: 0.176 / Highest resolution: 2.2 Å
Refinement stepCycle: LAST / Highest resolution: 2.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1772 0 42 130 1944
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.82
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 5 Å / Rfactor obs: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.82

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