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- PDB-1k2i: Crystal Structure of Gamma-Chymotrypsin in Complex with 7-Hydroxy... -

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Basic information

Entry
Database: PDB / ID: 1k2i
TitleCrystal Structure of Gamma-Chymotrypsin in Complex with 7-Hydroxycoumarin
ComponentsCHYMOTRYPSINOGEN A
KeywordsHYDROLASE / enzyme-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 / 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
2,4-DIHYDROXY-TRANS CINNAMIC ACID / Chymotrypsinogen A
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsGhani, U. / Ng, K.K.S. / Atta-ur-Rahman / Choudhary, M.I. / Ullah, N. / James, M.N.G.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of gamma-chymotrypsin in complex with 7-hydroxycoumarin.
Authors: Ghani, U. / Ng, K.K. / Atta-ur-Rahman / Choudhary, M.I. / Ullah, N. / James, M.N.
History
DepositionSep 27, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.4Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_distant_solvent_atoms / pdbx_entry_details ...pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: CHYMOTRYPSINOGEN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9623
Polymers25,6861
Non-polymers2762
Water2,414134
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
1: CHYMOTRYPSINOGEN A
hetero molecules

1: CHYMOTRYPSINOGEN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9256
Polymers51,3722
Non-polymers5524
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area3010 Å2
ΔGint-41 kcal/mol
Surface area18480 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)69.852, 69.852, 97.380
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
111-514-

HOH

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Components

#1: Protein CHYMOTRYPSINOGEN A


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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-SN1 / 2,4-DIHYDROXY-TRANS CINNAMIC ACID


Mass: 180.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.31 Å3/Da / Density % sol: 46.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: ammonium sulfate, sodium cacodylate, dioxane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
152 %(w/v)satammonium sulfate1reservoir
210 mg/mlenzyme1drop
30.1 Msodium cacodylate1droppH7.0
42.5 %(v/v)dioxane1drop

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Aug 17, 1999 / Details: double-focusing mirrors
RadiationMonochromator: Yale mirrors + Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 23275 / Num. obs: 22972 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 18.3
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 4.3 / Num. unique all: 2229 / Rsym value: 0.351 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 104762
Reflection shell
*PLUS
Highest resolution: 1.8 Å / % possible obs: 100 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1GCT

1gct


Resolution: 1.8→30 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1995 2241 9.9 %Random
Rwork0.1796 ---
all0.19 23007 --
obs0.19 22635 98.4 %-
Displacement parametersBiso mean: 16.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.658 Å20 Å20 Å2
2---0.658 Å20 Å2
3---1.316 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1735 0 17 134 1886
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.29
X-RAY DIFFRACTIONc_bond_d0.0045
X-RAY DIFFRACTIONc_mcangle_it1.706
X-RAY DIFFRACTIONc_mcbond_it1.152
Refinement
*PLUS
Lowest resolution: 30 Å / Num. reflection obs: 22933 / Rfactor obs: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS

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