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- PDB-8sj5: Walnut Tree Phytocystatin -

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Basic information

Entry
Database: PDB / ID: 8sj5
TitleWalnut Tree Phytocystatin
ComponentsCysteine proteinase inhibitor
KeywordsPROTEIN BINDING / Cystatin / Protease Inhibitor / regulatory
Function / homologyAspartic acid proteinase inhibitor / Cystatin / Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin-like domain / Cystatin domain / Cystatin superfamily / cysteine-type endopeptidase inhibitor activity / Cysteine proteinase inhibitor
Function and homology information
Biological speciesJuglans regia (English walnut)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsValadares, N.F.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Other government00193-00001131/2021-91 Brazil
Other government193.001.668/2017 Brazil
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2023
Title: Crystal structure and interconversion of monomers and domain-swapped dimers of the walnut tree phytocystatin.
Authors: Simpson, G.A. / Rezende, I.F. / da Silva Peixoto, A. / de Oliveira Soares, I.B. / Barbosa, J.A.R.G. / de Freitas, S.M. / Valadares, N.F.
History
DepositionApr 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cysteine proteinase inhibitor
C: Cysteine proteinase inhibitor
B: Cysteine proteinase inhibitor
D: Cysteine proteinase inhibitor


Theoretical massNumber of molelcules
Total (without water)45,4514
Polymers45,4514
Non-polymers00
Water0
1
A: Cysteine proteinase inhibitor
B: Cysteine proteinase inhibitor


Theoretical massNumber of molelcules
Total (without water)22,7262
Polymers22,7262
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-32 kcal/mol
Surface area10400 Å2
MethodPISA
2
C: Cysteine proteinase inhibitor
D: Cysteine proteinase inhibitor


Theoretical massNumber of molelcules
Total (without water)22,7262
Polymers22,7262
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-34 kcal/mol
Surface area10280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.767, 79.346, 63.914
Angle α, β, γ (deg.)90.000, 108.110, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
Cysteine proteinase inhibitor /


Mass: 11362.795 Da / Num. of mol.: 4 / Mutation: D11N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Juglans regia (English walnut) / Gene: LOC109000616 / Plasmid: pET-24a / Details (production host): between NdeI and XhoI / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2I4FN75

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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: 2.83 Å3/Da / Density % sol: 56.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 38 % v/v PEG 300, 0.2 M Na2HPO4, 0.1 M citric acid and pH 4.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER X8 PROTEUM / Wavelength: 1.54184 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Dec 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 3.1→46.74 Å / Num. obs: 9197 / % possible obs: 98.51 % / Redundancy: 2 % / Biso Wilson estimate: 58.47 Å2 / CC1/2: 0.996 / Net I/σ(I): 7.2
Reflection shellResolution: 3.104→3.215 Å / Num. unique obs: 904 / CC1/2: 0.723 / CC star: 0.916 / % possible all: 96.99

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Processing

Software
NameVersionClassification
XDS20190806data reduction
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→46.74 Å / SU ML: 0.4341 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.3961
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2986 460 5.03 %
Rwork0.2877 8685 -
obs0.2883 9145 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.57 Å2
Refinement stepCycle: LAST / Resolution: 3.1→46.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2645 0 0 0 2645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00342697
X-RAY DIFFRACTIONf_angle_d0.72833636
X-RAY DIFFRACTIONf_chiral_restr0.0466404
X-RAY DIFFRACTIONf_plane_restr0.0035455
X-RAY DIFFRACTIONf_dihedral_angle_d6.3868336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.550.33611520.30842865X-RAY DIFFRACTION98.47
3.55-4.480.27641530.29152903X-RAY DIFFRACTION99.09
4.48-46.740.29541550.27472917X-RAY DIFFRACTION98.15

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