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- PDB-8zlq: Proenzyme of Triticum aestivum papain-like cysteine protease Trit... -

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Basic information

Entry
Database: PDB / ID: 8zlq
TitleProenzyme of Triticum aestivum papain-like cysteine protease Triticain-alpha inactive mutant lacking granulin domain
ComponentsTriticain alpha
KeywordsHYDROLASE / Cysteine protease / glutenase / seed germination
Function / homology
Function and homology information


cysteine-type peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis
Similarity search - Function
Granulin / Granulin superfamily / Granulin / Granulin / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. ...Granulin / Granulin superfamily / Granulin / Granulin / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Biological speciesTriticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.46 Å
AuthorsPetushkova, A.I. / Zalevsky, A.O. / Gorokhovets, N.V. / Makarov, V.A. / Maslova, V.D. / Fedorov, V.A. / Savvateeva, L.V. / Zernii, E.Y. / Soond, S.M. / Golovin, A.V. / Zamyatnin Jr., A.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Structure of Triticain-Alpha Revealed a pH-Dependent Mechanism of Substrate Recognition
Authors: Petushkova, A.I. / Zalevsky, A.O. / Gorokhovets, N.V. / Makarov, V.A. / Maslova, V.D. / Fedorov, V.A. / Savvateeva, L.V. / Zernii, E.Y. / Soond, S.M. / Golovin, A.V. / Zamyatnin Jr., A.A.
History
DepositionMay 21, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Triticain alpha


Theoretical massNumber of molelcules
Total (without water)38,3691
Polymers38,3691
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.691, 126.691, 42.361
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

#1: Protein Triticain alpha


Mass: 38369.215 Da / Num. of mol.: 1 / Mutation: C154A
Source method: isolated from a genetically manipulated source
Details: Engineered mutation: C154A. Expression tag: first 20 aa contain His-tag; they were not modelled due to low resolution.
Source: (gene. exp.) Triticum aestivum (bread wheat) / Organ: SEEDLING / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami 2 (DE3) pLysS
References: UniProt: Q0WXG8, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
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: 2.56 Å3/Da / Density % sol: 51.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 100 mM sodium acetate buffer, 3.5% polyethylene glycol 4000 (w/v), 15% glycerol (v/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.96409 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96409 Å / Relative weight: 1
ReflectionResolution: 3.46→109.72 Å / Num. obs: 4186 / % possible obs: 78.6 % / Redundancy: 1.9 % / Biso Wilson estimate: 131.38 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.059 / Rrim(I) all: 0.083 / Χ2: 0.88 / Net I/σ(I): 9.4
Reflection shellResolution: 3.46→3.79 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 382 / CC1/2: 0.787 / Rpim(I) all: 0.54 / Rrim(I) all: 0.764 / Χ2: 0.94 / % possible all: 29.5

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Processing

Software
NameVersionClassification
autoPROC1.0.5 (20190923)data reduction
STARANISO2.3.13 (20190907)data scaling
PHENIX1.21_5207phasing
PHENIX1.21_5207refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AF-Q0WXG8-F1

Resolution: 3.46→109.7 Å / SU ML: 0.1804 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.2482
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2594 221 -
Rwork0.2441 7355 -
obs-4178 78.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 164.76 Å2
Refinement stepCycle: LAST / Resolution: 3.46→109.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2548 0 0 0 2548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00152597
X-RAY DIFFRACTIONf_angle_d0.41533506
X-RAY DIFFRACTIONf_chiral_restr0.0383360
X-RAY DIFFRACTIONf_plane_restr0.0028471
X-RAY DIFFRACTIONf_dihedral_angle_d8.9901959
LS refinement shellResolution: 3.46→3.96 Å
RfactorNum. reflection% reflection
Rfree0.4207 37 -
Rwork0.4216 706 -
obs--39.21 %
Refinement TLS params.Method: refined / Origin x: -10.8162098673 Å / Origin y: -48.01247437 Å / Origin z: 1.56756106857 Å
111213212223313233
T1.23625932209 Å20.114668199272 Å20.04547966457 Å2-1.0218441637 Å20.0343305001649 Å2--0.721893684405 Å2
L5.10023058536 °2-2.86512546871 °21.00280503993 °2-3.50491094059 °2-1.27230822418 °2--3.65207340012 °2
S-0.166095183967 Å °0.678386932523 Å °0.605094947926 Å °0.742595757411 Å °-0.0837918619314 Å °-0.226844879862 Å °-1.19943762166 Å °-0.144683113657 Å °-0.00544856455548 Å °
Refinement TLS groupSelection details: all

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