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- PDB-1gg6: CRYSTAL STRUCTURE OF GAMMA CHYMOTRYPSIN WITH N-ACETYL-PHENYLALANI... -

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Basic information

Entry
Database: PDB / ID: 1gg6
TitleCRYSTAL STRUCTURE OF GAMMA CHYMOTRYPSIN WITH N-ACETYL-PHENYLALANINE TRIFLUOROMETHYL KETONE BOUND AT THE ACTIVE SITE
Components(GAMMA CHYMOTRYPSIN) x 3
KeywordsHYDROLASE/HYDROLASE INHIBITOR / CHYMOTRYPSIN / 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 / 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
Chem-APF / Chem-APL / Chymotrypsinogen A
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.4 Å
AuthorsNeidhart, D. / Wei, Y. / Cassidy, C. / Lin, J. / Cleland, W.W. / Frey, P.A.
CitationJournal: Biochemistry / Year: 2001
Title: Correlation of low-barrier hydrogen bonding and oxyanion binding in transition state analogue complexes of chymotrypsin.
Authors: Neidhart, D. / Wei, Y. / Cassidy, C. / Lin, J. / Cleland, W.W. / Frey, P.A.
History
DepositionJul 31, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)26,07812
Polymers25,0053
Non-polymers1,0739
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9480 Å2
ΔGint-98 kcal/mol
Surface area9960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.190, 69.190, 95.440
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-654-

HOH

21B-718-

HOH

31C-572-

HOH

41C-723-

HOH

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Components

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Protein/peptide , 1 types, 1 molecules A

#1: Protein/peptide GAMMA CHYMOTRYPSIN


Mass: 996.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P00766, chymotrypsin

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Protein , 2 types, 2 molecules BC

#2: Protein GAMMA CHYMOTRYPSIN


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


Mass: 10074.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P00766, chymotrypsin

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Non-polymers , 5 types, 342 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-APL / N-(1-BENZYL-3,3,3-TRIFLUORO-2,2-DIHYDROXY-PROPYL)-ACETAMIDE


Mass: 277.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H14F3NO3
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-APF / 1,1,1-TRIFLUORO-3-ACETAMIDO-4-PHENYL BUTAN-2-ONE(N-ACETYL-L-PHENYLALANYL TRIFLUOROMETHYL KETONE)


Mass: 259.224 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H12F3NO2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O

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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: 2.28 Å3/Da / Density % sol: 46.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: ammonium sulfate, potassium phosphate, pH 7.0, vapor diffusion, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
175 %satammonium sulfate1reservoir
210 mMpotassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Nov 29, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. all: 45082 / Num. obs: 42041 / % possible obs: 91.4 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.027
Reflection shellResolution: 1.4→1.45 Å / Rmerge(I) obs: 0.118 / % possible all: 75.8
Reflection
*PLUS
Num. obs: 45082
Reflection shell
*PLUS
% possible obs: 75.8 %

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Processing

Software
NameVersionClassification
FRAMBOdata collection
XDSdata reduction
XCALIBREmodel building
X-PLOR3.5refinement
XDSdata scaling
XCALIBREphasing
RefinementResolution: 1.4→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: Initial coordinates for this structure were derived from the model of G. Cohen et al. (PDB entry 2GCH). Secondary structure elements and sequence data are identical to those of entry 2GCH ...Details: Initial coordinates for this structure were derived from the model of G. Cohen et al. (PDB entry 2GCH). Secondary structure elements and sequence data are identical to those of entry 2GCH except that the use of cryocrystallography techniques and the extended resolution of the current study permitted assignment of coordinates to residues 149 and 150, which are adjacent to a natural excission site. Initial phases were derived from the 2GCH model. A previous entry by Brady et al. (PDB entry 6gch) describes an identical complex determined by crystal structure analysis at lower resolution (2.1 Angstrom). More accurate determination of hydrogen bonding distances within the catalytic triad motivated the current study.
RfactorNum. reflection% reflection
Rfree0.212 4230 -
Rwork0.175 --
all-45082 -
obs-42041 91.4 %
Refinement stepCycle: LAST / Resolution: 1.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1751 0 68 333 2152
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.4
Software
*PLUS
Name: X-PLOR / Version: 3.5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.4

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