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

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Basic information

Entry
Database: PDB / ID: 1gcd
TitleREFINED CRYSTAL STRUCTURE OF "AGED" AND "NON-AGED" ORGANOPHOSPHORYL CONJUGATES OF GAMMA-CHYMOTRYPSIN
ComponentsGAMMA-CHYMOTRYPSIN
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
DIETHYL PHOSPHONATE / Chymotrypsinogen A
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.9 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
DepositionMay 5, 1994Processing site: BNL
Revision 1.0Jun 22, 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 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GAMMA-CHYMOTRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1125
Polymers25,6861
Non-polymers4264
Water5,008278
1
A: GAMMA-CHYMOTRYPSIN
hetero molecules

A: GAMMA-CHYMOTRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,22510
Polymers51,3722
Non-polymers8538
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)69.000, 69.000, 95.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein GAMMA-CHYMOTRYPSIN


Mass: 25686.037 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P00766, chymotrypsin
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DEP / DIETHYL PHOSPHONATE


Mass: 138.102 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H11O3P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsCOVALENTLY BOUND DIETHYL PHOSPHORYL MOIETY (PARAOXON) DEP 290: C4-C3-O2-P-O1-C1-C2 | O4
Sequence detailsAMINO ACID SEQUENCE FOR THIS ENTRY IS TAKEN FROM BLOW ET AL., NATURE, 221, 337 (1969).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.27 %
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: 1.9 Å / Num. obs: 16854 / Num. measured all: 17990 / Rmerge(I) obs: 0.025

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.9→6 Å / σ(F): 0 /
RfactorNum. reflection
obs0.187 16171
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1744 0 23 278 2045
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.025
X-RAY DIFFRACTIONp_angle_d0.0310.035
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0360.05
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_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
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
Num. reflection all: 16171 / Rfactor all: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS

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