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- PDB-5gqt: Crystal structure of a specifier Protein from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 5gqt
TitleCrystal structure of a specifier Protein from Arabidopsis thaliana
ComponentsNitrile-specifier protein 1
KeywordsPLANT PROTEIN / beta sheet / beta propeller
Function / homology
Function and homology information


nitrile biosynthetic process / response to herbivore / glucosinolate catabolic process / enzyme regulator activity / carbohydrate binding / mRNA binding / nucleus / cytosol
Similarity search - Function
Nitrile-specifier protein 1/2/3 / Galactose oxidase, central domain / Jacalin-like lectin domain, plant / Jacalin-like lectin domain / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-type lectin domain profile. ...Nitrile-specifier protein 1/2/3 / Galactose oxidase, central domain / Jacalin-like lectin domain, plant / Jacalin-like lectin domain / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Jacalin-like lectin domain superfamily / Kelch / Kelch repeat type 1 / Kelch motif / Kelch-type beta propeller / Mainly Beta
Similarity search - Domain/homology
Nitrile-specifier protein 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.022 Å
AuthorsZhang, W. / Feng, Y.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Crystal structure of the nitrile-specifier protein NSP1 from Arabidopsis thaliana
Authors: Zhang, W. / Zhou, Y. / Wang, K. / Dong, Y. / Wang, W. / Feng, Y.
History
DepositionAug 8, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitrile-specifier protein 1


Theoretical massNumber of molelcules
Total (without water)52,8011
Polymers52,8011
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18930 Å2
Unit cell
Length a, b, c (Å)120.902, 120.902, 123.006
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Nitrile-specifier protein 1 / AtNSP1 / Jacalin-related lectin 28


Mass: 52800.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: NSP1, JAL28, At3g16400, MDC8.2, T02O04.11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SDM9

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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: 4.92 Å3/Da / Density % sol: 74.98 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: ammonium acetate, bis-tris propane pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.02→50 Å / Num. obs: 20806 / % possible obs: 99.9 % / Redundancy: 12 % / Net I/σ(I): 19.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 3.022→37.673 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 30.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2672 931 4.92 %
Rwork0.227 --
obs0.229 18913 48.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.022→37.673 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3542 0 0 0 3542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113626
X-RAY DIFFRACTIONf_angle_d1.4384908
X-RAY DIFFRACTIONf_dihedral_angle_d16.2351245
X-RAY DIFFRACTIONf_chiral_restr0.057518
X-RAY DIFFRACTIONf_plane_restr0.005639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0218-3.1810.3164730.27921359X-RAY DIFFRACTION26
3.181-3.38020.344960.27151964X-RAY DIFFRACTION37
3.3802-3.6410.33551490.26892725X-RAY DIFFRACTION51
3.641-4.00710.2751360.26222807X-RAY DIFFRACTION52
4.0071-4.5860.21961600.18762801X-RAY DIFFRACTION53
4.586-5.77450.22611490.19762885X-RAY DIFFRACTION54
5.7745-37.67560.28291680.22743441X-RAY DIFFRACTION64

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