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- PDB-7x8j: Arabidopsis GDP-D-mannose pyrophosphorylase (VTC1) structure (unl... -

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Basic information

Entry
Database: PDB / ID: 7x8j
TitleArabidopsis GDP-D-mannose pyrophosphorylase (VTC1) structure (unliganded)
ComponentsMannose-1-phosphate guanylyltransferase 1
KeywordsTRANSFERASE / ascorbic acid / nucleotide sugar / guanylyltransferase / Arabidopsis thaliana
Function / homology
Function and homology information


mannose-1-phosphate guanylyltransferase / mannose-1-phosphate guanylyltransferase (GTP) activity / L-ascorbic acid biosynthetic process / cellulose biosynthetic process / GDP-mannose biosynthetic process / response to ammonium ion / response to ozone / response to jasmonic acid / response to salt stress / response to heat ...mannose-1-phosphate guanylyltransferase / mannose-1-phosphate guanylyltransferase (GTP) activity / L-ascorbic acid biosynthetic process / cellulose biosynthetic process / GDP-mannose biosynthetic process / response to ammonium ion / response to ozone / response to jasmonic acid / 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 / : / GMPPB C-terminal domain / : / Hexapeptide-repeat containing-transferases signature. / Nucleotidyl transferase domain / Nucleotidyl transferase / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / 3 Solenoid ...Mannose-1-phosphate guanyltransferase, N-terminal domain / : / GMPPB C-terminal domain / : / Hexapeptide-repeat containing-transferases signature. / Nucleotidyl transferase domain / Nucleotidyl transferase / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / 3 Solenoid / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Mannose-1-phosphate guanylyltransferase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.798 Å
AuthorsZhao, S. / Zhang, C. / Liu, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Front Plant Sci / Year: 2022
Title: Crystal Structures of Arabidopsis thaliana GDP-D-Mannose Pyrophosphorylase VITAMIN C DEFECTIVE 1.
Authors: Zhang, C. / Zhao, S. / Li, Y.S. / He, C. / Wang, X. / Liu, L.
History
DepositionMar 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mannose-1-phosphate guanylyltransferase 1
B: Mannose-1-phosphate guanylyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,31319
Polymers82,6802
Non-polymers1,63317
Water55831
1
A: Mannose-1-phosphate guanylyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,30111
Polymers41,3401
Non-polymers96110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-14 kcal/mol
Surface area15250 Å2
MethodPISA
2
B: Mannose-1-phosphate guanylyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0138
Polymers41,3401
Non-polymers6727
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint-38 kcal/mol
Surface area15260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.519, 146.862, 70.860
Angle α, β, γ (deg.)90.000, 100.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: 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: 41340.145 Da / Num. of mol.: 2
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
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.76 Å3/Da / Density % sol: 55.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: bis-tris, PEG 3350, lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.798→50 Å / Num. obs: 21924 / % possible obs: 99.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 63.63 Å2 / CC1/2: 0.967 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.047 / Net I/σ(I): 16.1
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2165 / CC1/2: 0.881 / Rpim(I) all: 0.31 / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7D72

7d72


Resolution: 2.798→32.633 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 31.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2582 1091 4.99 %
Rwork0.2148 20788 -
obs0.2169 21879 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.53 Å2 / Biso mean: 63.7663 Å2 / Biso min: 37.31 Å2
Refinement stepCycle: final / Resolution: 2.798→32.633 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5430 0 85 31 5546
Biso mean--74.26 57.48 -
Num. residues----713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035606
X-RAY DIFFRACTIONf_angle_d0.5647610
X-RAY DIFFRACTIONf_chiral_restr0.049881
X-RAY DIFFRACTIONf_plane_restr0.004951
X-RAY DIFFRACTIONf_dihedral_angle_d19.9212069
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.798-2.92520.351440.3006247496
2.9252-3.07930.38321460.30792605100
3.0793-3.27210.35171280.28752604100
3.2721-3.52440.34841340.252621100
3.5244-3.87860.26771390.22282595100
3.8786-4.43860.21391340.19182645100
4.4386-5.58770.2081320.1766260499
5.5877-32.6330.22181340.1885264099

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