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- PDB-1yph: High resolution structure of bovine alpha-chymotrypsin -

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Basic information

Entry
Database: PDB / ID: 1yph
TitleHigh resolution structure of bovine alpha-chymotrypsin
Components
  • CHYMOTRYPSIN A, chain A
  • CHYMOTRYPSIN A, chain B
  • CHYMOTRYPSIN A, chain C
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 / 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
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsRazeto, A. / Galunsky, B. / Kasche, V. / Wilson, K.S. / Lamzin, V.S.
CitationJournal: To be Published
Title: High resolution structure of native bovine alpha-chymotrypsin
Authors: Razeto, A. / Galunsky, B. / Kasche, V. / Wilson, K.S. / Lamzin, V.S.
History
DepositionJan 31, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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

Downloads & links

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Assembly

Deposited unit
A: CHYMOTRYPSIN A, chain A
C: CHYMOTRYPSIN A, chain B
E: CHYMOTRYPSIN A, chain C
B: CHYMOTRYPSIN A, chain A
D: CHYMOTRYPSIN A, chain B
F: CHYMOTRYPSIN A, chain C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,00511
Polymers50,5256
Non-polymers4805
Water10,917606
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18070 Å2
ΔGint-209 kcal/mol
Surface area17520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.83, 77.51, 62.77
Angle α, β, γ (deg.)90.0, 106.3, 90.0
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide CHYMOTRYPSIN A, chain A / alpha-chymotrypsin / Chymotrypsinogen A


Mass: 1253.511 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00766, chymotrypsin
#2: Protein CHYMOTRYPSIN A, chain B / alpha-chymotrypsin / Chymotrypsinogen A


Mass: 13934.556 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00766, chymotrypsin
#3: Protein CHYMOTRYPSIN A, chain C / alpha-chymotrypsin / Chymotrypsinogen A


Mass: 10074.495 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00766, chymotrypsin
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 606 / 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: 2.05 Å3/Da / Density % sol: 39.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: PEG 1500, Ammonium sulphate, citrate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.91 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 20, 1997
Details: triagular horizontal focusing Si (111) monochromator and bent mirror
RadiationMonochromator: triagular horizontal focusing Si (111) monochromator and bent mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.34→28.6 Å / Num. all: 87580 / Num. obs: 87580 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 19.6
Reflection shellResolution: 1.34→1.41 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 2.1 / Num. unique all: 11767 / % possible all: 95.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5CHA molecule B

5cha


Resolution: 1.34→28.6 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.055 / ESU R Free: 0.059 / Stereochemistry target values: Engh & Huber
Details: used restrained refinement by minimisation of a maximum-likelihood target function as in REFMAC
RfactorNum. reflection% reflectionSelection details
Rfree0.189 4391 5 %RANDOM
Rwork0.139 ---
obs0.139 87580 97.1 %-
all-87580 --
Displacement parametersBiso mean: 19.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.059 Å0.055 Å
Refinement stepCycle: LAST / Resolution: 1.34→28.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3657 0 25 606 4288
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0340.04
X-RAY DIFFRACTIONp_planar_d0.0380.05
X-RAY DIFFRACTIONp_plane_restr0.0270.03
X-RAY DIFFRACTIONp_chiral_restr0.0940.15
X-RAY DIFFRACTIONp_singtor_nbd0.1570.3
X-RAY DIFFRACTIONp_multtor_nbd0.2350.3
X-RAY DIFFRACTIONp_special_tor015
X-RAY DIFFRACTIONp_planar_tor5.17
X-RAY DIFFRACTIONp_staggered_tor12.315
X-RAY DIFFRACTIONp_transverse_tor22.220
X-RAY DIFFRACTIONp_mcbond_it2.5312
X-RAY DIFFRACTIONp_mcangle_it3.333
X-RAY DIFFRACTIONp_scbond_it3.0382
X-RAY DIFFRACTIONp_scangle_it4.0223
LS refinement shellResolution: 1.34→1.41 Å
RfactorNum. reflection% reflection
Rfree0.254 614 -
Rwork0.198 --
obs-11767 96.4 %

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