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- PDB-8yre: Crystal structure of Arabidopsis VTC1-KJC2 -

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Basic information

Entry
Database: PDB / ID: 8yre
TitleCrystal structure of Arabidopsis VTC1-KJC2
Components
  • ADP-glucose pyrophosphorylase family protein
  • Mannose-1-phosphate guanylyltransferase 1
KeywordsTRANSFERASE / nucleotide sugar / oligomerization / allostery / VTC1 / KJC2
Function / homology
Function and homology information


regulation of L-ascorbic acid biosynthetic process / mannose-1-phosphate guanylyltransferase / mannose-1-phosphate guanylyltransferase (GTP) activity / L-ascorbic acid biosynthetic process / cellulose biosynthetic process / response to ammonium ion / GDP-mannose biosynthetic process / response to jasmonic acid / response to ozone / biosynthetic process ...regulation of L-ascorbic acid biosynthetic process / mannose-1-phosphate guanylyltransferase / mannose-1-phosphate guanylyltransferase (GTP) activity / L-ascorbic acid biosynthetic process / cellulose biosynthetic process / response to ammonium ion / GDP-mannose biosynthetic process / response to jasmonic acid / response to ozone / biosynthetic process / response to salt stress / response to heat / defense response to bacterium / GTP binding / nucleus / cytosol
Similarity search - Function
Mannose-1-phosphate guanyltransferase, N-terminal domain / : / Hexapeptide-repeat containing-transferases signature. / Nucleotidyl transferase domain / Nucleotidyl transferase / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
ADP-glucose pyrophosphorylase family protein / Mannose-1-phosphate guanylyltransferase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.54 Å
AuthorsZhang, C. / Liu, L.
Funding support China, 1items
OrganizationGrant numberCountry
Not funded China
CitationJournal: To Be Published
Title: Structural insight into the regulation of GDP-mannose pyrophosphorylase activity of Arabidopsis KJC2-VTC1 complex
Authors: Zhang, C. / Liu, L.
History
DepositionMar 21, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADP-glucose pyrophosphorylase family protein
B: ADP-glucose pyrophosphorylase family protein
C: ADP-glucose pyrophosphorylase family protein
D: Mannose-1-phosphate guanylyltransferase 1
E: Mannose-1-phosphate guanylyltransferase 1
F: Mannose-1-phosphate guanylyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,99418
Polymers253,8416
Non-polymers1,15312
Water362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)158.268, 134.987, 168.473
Angle α, β, γ (deg.)90.00, 117.14, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ADP-glucose pyrophosphorylase family protein


Mass: 44988.461 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: KJC2, At2g04650, F28I8.31, F28I8_31 / Production host: Escherichia coli (E. coli) / References: UniProt: F4IFA4
#2: Protein Mannose-1-phosphate guanylyltransferase 1 / GDP-mannose pyrophosphorylase 1 / Protein CYTOKINESIS DEFECTIVE 1 / Protein EMBRYO DEFECTIVE 101 / ...GDP-mannose pyrophosphorylase 1 / Protein CYTOKINESIS DEFECTIVE 1 / Protein EMBRYO DEFECTIVE 101 / Protein HYPERSENSITIVE TO AMMONIUM ION 1 / Protein SENSITIVE TO OZONE 1 / Protein VITAMIN C DEFECTIVE 1


Mass: 39625.184 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress)
Gene: CYT1, EMB101, GMP1, HSN1, SOZ1, VTC1, At2g39770, T5I7.7
Production host: Escherichia coli (E. coli)
References: UniProt: O22287, mannose-1-phosphate guanylyltransferase
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 3.15 Å3/Da / Density % sol: 61.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: ammonium sulphate, Bis-Tris propane, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 3.54→149.92 Å / Num. obs: 37074 / % possible obs: 96.4 % / Redundancy: 5 % / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.075 / Net I/σ(I): 7.8
Reflection shellResolution: 3.54→3.64 Å / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 5264 / CC1/2: 0.768 / Rpim(I) all: 0.467

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Processing

Software
NameVersionClassification
PHENIX1.18refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.54→149.92 Å / Cross valid method: FREE R-VALUE / σ(F): 319.39 / Phase error: 38.04 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2952 1918 5.34 %
Rwork0.2608 --
obs0.2638 37069 96.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.54→149.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17135 0 60 2 17197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00317527
X-RAY DIFFRACTIONf_angle_d0.56223780
X-RAY DIFFRACTIONf_dihedral_angle_d13.3186488
X-RAY DIFFRACTIONf_chiral_restr0.0482768
X-RAY DIFFRACTIONf_plane_restr0.0043014
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.54-3.630.32461590.32462582X-RAY DIFFRACTION94
3.63-3.730.34571310.32132259X-RAY DIFFRACTION82
3.73-3.840.30681590.30682560X-RAY DIFFRACTION94
3.84-3.960.3634990.31371674X-RAY DIFFRACTION61
3.96-4.110.33651200.30222626X-RAY DIFFRACTION96
4.11-4.270.33861270.28622595X-RAY DIFFRACTION95
4.27-4.460.30261330.26982579X-RAY DIFFRACTION95
4.46-4.70.31611340.25862623X-RAY DIFFRACTION95
4.7-4.990.25471610.25472576X-RAY DIFFRACTION94
4.99-5.380.29531290.26652603X-RAY DIFFRACTION95
5.38-5.920.33991260.27732609X-RAY DIFFRACTION95
5.92-6.780.33241300.28442641X-RAY DIFFRACTION95
6.78-8.540.30111470.23112610X-RAY DIFFRACTION94
8.54-149.920.25521620.19972615X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: 26.7016 Å / Origin y: -31.6623 Å / Origin z: 35.7332 Å
111213212223313233
T0.5464 Å20.0403 Å2-0.0667 Å2-0.9514 Å20.034 Å2--0.8298 Å2
L0.6039 °2-0.0146 °20.0628 °2-0.7109 °20.1185 °2--0.4541 °2
S0.0121 Å °0.0093 Å °-0.1018 Å °0.3724 Å °0.0468 Å °-0.1192 Å °0.1203 Å °0.0365 Å °-0.0525 Å °
Refinement TLS groupSelection details: all

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