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- PDB-5r4d: Crystal Structure of gamma-Chymotrypsin at pH 9, cryo temperature -

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Basic information

Entry
Database: PDB / ID: 5r4d
TitleCrystal Structure of gamma-Chymotrypsin at pH 9, cryo temperature
Components
  • (gamma-chymotrypsin) x 3
  • peptide GSWPW
  • peptide TPGVY
KeywordsHYDROLASE / serine protease / hydrolase-peptide 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 family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
IODIDE ION / Chymotrypsinogen A
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.05 Å
AuthorsKreinbring, C.A. / Wilson, M.A. / Kovalevsky, A.Y. / Blakeley, M.P. / Fisher, S.Z. / Lazar, L.M. / Moulin, A.G. / Novak, W.R. / Petsko, G.A. / Ringe, D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM32415 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM26788 United States
CitationJournal: To be published
Title: Effect of Temperature and pH on Ionizable Residues in gamma-Chymotrypsin: a X-ray and Neutron Crystallography Study
Authors: Kreinbring, C.A. / Wilson, M.A. / Kovalevsky, A.Y. / Blakeley, M.P. / Fisher, S.Z. / Lazar, L.M. / Moulin, A.G. / Novak, W.R. / Petsko, G.A. / Ringe, D.
History
DepositionFeb 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: gamma-chymotrypsin
B: gamma-chymotrypsin
C: gamma-chymotrypsin
D: peptide GSWPW
E: peptide TPGVY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,97210
Polymers26,4305
Non-polymers5425
Water7,026390
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.067, 69.067, 95.803
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-201-

IOD

21B-202-

IOD

31B-370-

HOH

41B-518-

HOH

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Components

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Protein/peptide , 3 types, 3 molecules ADE

#1: Protein/peptide gamma-chymotrypsin


Mass: 1253.511 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00766, chymotrypsin
#4: Protein/peptide peptide GSWPW


Mass: 631.679 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)
#5: Protein/peptide peptide TPGVY


Mass: 535.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)

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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) / 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) / References: UniProt: P00766, chymotrypsin

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Non-polymers , 3 types, 395 molecules

#6: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.25 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: 45% saturated ammonium sulfate, 0.75% saturated cetyltrimethylammonium bromide, 100 mM sodium iodide; sodium malonate
PH range: 10 mM sodium cacodylate pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.05→50 Å / Num. obs: 107355 / % possible obs: 99.2 % / Redundancy: 16.7 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 12.3
Reflection shellResolution: 1.05→1.09 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.766 / % possible all: 93.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0158refinement
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1GCT

1gct


Resolution: 1.05→56.03 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.666 / SU ML: 0.015 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.023 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.14 5388 5 %RANDOM
Rwork0.122 ---
obs0.123 101897 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2--0.41 Å20 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 1.05→56.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1833 0 17 390 2240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022123
X-RAY DIFFRACTIONr_bond_other_d0.0030.021941
X-RAY DIFFRACTIONr_angle_refined_deg1.6481.9452929
X-RAY DIFFRACTIONr_angle_other_deg1.09434548
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0255294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.45925.77571
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.71615338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.39153
X-RAY DIFFRACTIONr_chiral_restr0.0980.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212380
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02399
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.30634063
X-RAY DIFFRACTIONr_sphericity_free34.8195228
X-RAY DIFFRACTIONr_sphericity_bonded12.70754164
LS refinement shellResolution: 1.05→1.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 385 -
Rwork0.297 6801 -
obs--90.89 %

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