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- PDB-1gmh: REFINED CRYSTAL STRUCTURE OF "AGED" AND "NON-AGED" ORGANOPHOSPHOR... -

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Basic information

Entry
Database: PDB / ID: 1gmh
TitleREFINED CRYSTAL STRUCTURE OF "AGED" AND "NON-AGED" ORGANOPHOSPHORYL CONJUGATES OF GAMMA-CHYMOTRYPSIN
Components(GAMMA-CHYMOTRYPSIN ...) x 3
KeywordsHYDROLASE(SERINE PROTEINASE)
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
PHOSPHORYLISOPROPANE / Chymotrypsinogen A
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsHarel, M. / Sussman, J.L. / Silman, I.
Citation
Journal: J.Mol.Biol. / Year: 1991
Title: Refined crystal structures of "aged" and "non-aged" organophosphoryl conjugates of gamma-chymotrypsin.
Authors: Harel, M. / Su, C.T. / Frolow, F. / Ashani, Y. / Silman, I. / Sussman, J.L.
#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.
History
DepositionJul 1, 1994Processing site: BNL
Revision 1.0Sep 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 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 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: GAMMA-CHYMOTRYPSIN A
F: GAMMA-CHYMOTRYPSIN A
G: GAMMA-CHYMOTRYPSIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5956
Polymers25,2633
Non-polymers3323
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7860 Å2
ΔGint-86 kcal/mol
Surface area9980 Å2
MethodPISA
2
E: GAMMA-CHYMOTRYPSIN A
F: GAMMA-CHYMOTRYPSIN A
G: GAMMA-CHYMOTRYPSIN A
hetero molecules

E: GAMMA-CHYMOTRYPSIN A
F: GAMMA-CHYMOTRYPSIN A
G: GAMMA-CHYMOTRYPSIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,19012
Polymers50,5256
Non-polymers6646
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area17470 Å2
ΔGint-188 kcal/mol
Surface area18200 Å2
MethodPISA
3
E: GAMMA-CHYMOTRYPSIN A

E: GAMMA-CHYMOTRYPSIN A

F: GAMMA-CHYMOTRYPSIN A
G: GAMMA-CHYMOTRYPSIN A
hetero molecules

F: GAMMA-CHYMOTRYPSIN A
G: GAMMA-CHYMOTRYPSIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,19012
Polymers50,5256
Non-polymers6646
Water1086
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 area15930 Å2
ΔGint-175 kcal/mol
Surface area19740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.900, 69.900, 96.700
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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Non-polymers , 3 types, 105 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ISP / PHOSPHORYLISOPROPANE


Mass: 140.075 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9O4P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.34 Å3/Da / Density % sol: 47.37 %
Crystal grow
*PLUS
pH: 5.5 / Method: unknown / Details: Cohen, G.H., (1981) J. Mol. Biol., 148, 449.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112.5 mg/mlprotein11
250 %satammonium sulfate11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. all: 31167 / Num. obs: 11120 / Observed criterion σ(F): 3 / Rmerge(I) obs: 0.068

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Processing

SoftwareName: PROLSQ / Version: 1GMH / Classification: refinement
RefinementResolution: 2.1→6 Å / σ(F): 0 /
RfactorNum. reflection
obs0.187 11120
Refinement stepCycle: LAST / Resolution: 2.1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1741 0 17 102 1860
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.025
X-RAY DIFFRACTIONp_angle_d0.0270.031
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0350.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.010.02
X-RAY DIFFRACTIONp_chiral_restr0.120.15
X-RAY DIFFRACTIONp_singtor_nbd0.1830.5
X-RAY DIFFRACTIONp_multtor_nbd0.2010.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor1.72.8
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS

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