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- PDB-7x8k: Arabidopsis GDP-D-mannose pyrophosphorylase (VTC1) structure (pro... -

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Basic information

Entry
Database: PDB / ID: 7x8k
TitleArabidopsis GDP-D-mannose pyrophosphorylase (VTC1) structure (product-bound)
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 / cellulose biosynthetic process / cell wall mannoprotein biosynthetic process / GDP-mannose biosynthetic process / response to ammonium ion / response to jasmonic acid / response to ozone / L-ascorbic acid biosynthetic process / protein glycosylation ...mannose-1-phosphate guanylyltransferase / mannose-1-phosphate guanylyltransferase (GTP) activity / cellulose biosynthetic process / cell wall mannoprotein biosynthetic process / GDP-mannose biosynthetic process / response to ammonium ion / response to jasmonic acid / response to ozone / L-ascorbic acid biosynthetic process / protein glycosylation / response to salt stress / nucleotidyltransferase activity / response to heat / defense response to bacterium / GTP binding / nucleus / cytosol / cytoplasm
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
CITRATE ANION / GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE / PYROPHOSPHATE / Mannose-1-phosphate guanylyltransferase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)168,52528
Polymers165,3614
Non-polymers3,16524
Water19811
1
A: Mannose-1-phosphate guanylyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7119
Polymers41,3401
Non-polymers1,3718
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16070 Å2
MethodPISA
2
B: Mannose-1-phosphate guanylyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9987
Polymers41,3401
Non-polymers6586
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-13 kcal/mol
Surface area16300 Å2
MethodPISA
3
C: Mannose-1-phosphate guanylyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9136
Polymers41,3401
Non-polymers5735
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15630 Å2
MethodPISA
4
D: Mannose-1-phosphate guanylyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9026
Polymers41,3401
Non-polymers5625
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.113, 185.113, 371.752
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 81 or (resid 82...
21(chain B and (resid 1 through 81 or (resid 82...
31(chain C and (resid 1 through 9 or (resid 10...
41(chain D and (resid 1 through 151 or (resid 152...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETTHRTHR(chain A and (resid 1 through 81 or (resid 82...AA1 - 813 - 83
12GLUGLUGLUGLU(chain A and (resid 1 through 81 or (resid 82...AA8284
13METMETALAALA(chain A and (resid 1 through 81 or (resid 82...AA1 - 3663 - 368
14METMETALAALA(chain A and (resid 1 through 81 or (resid 82...AA1 - 3663 - 368
15METMETALAALA(chain A and (resid 1 through 81 or (resid 82...AA1 - 3663 - 368
16METMETALAALA(chain A and (resid 1 through 81 or (resid 82...AA1 - 3663 - 368
21METMETTHRTHR(chain B and (resid 1 through 81 or (resid 82...BB1 - 813 - 83
22GLUGLUGLUGLU(chain B and (resid 1 through 81 or (resid 82...BB8284
23METMETPPVPPV(chain B and (resid 1 through 81 or (resid 82...BB - R1 - 5063
24METMETPPVPPV(chain B and (resid 1 through 81 or (resid 82...BB - R1 - 5063
25METMETPPVPPV(chain B and (resid 1 through 81 or (resid 82...BB - R1 - 5063
26METMETPPVPPV(chain B and (resid 1 through 81 or (resid 82...BB - R1 - 5063
31METMETGLYGLY(chain C and (resid 1 through 9 or (resid 10...CC1 - 93 - 11
32PHEPHEPHEPHE(chain C and (resid 1 through 9 or (resid 10...CC1012
33METMETPROPRO(chain C and (resid 1 through 9 or (resid 10...CC1 - 3573 - 359
34METMETPROPRO(chain C and (resid 1 through 9 or (resid 10...CC1 - 3573 - 359
35METMETPROPRO(chain C and (resid 1 through 9 or (resid 10...CC1 - 3573 - 359
36METMETPROPRO(chain C and (resid 1 through 9 or (resid 10...CC1 - 3573 - 359
41METMETGLUGLU(chain D and (resid 1 through 151 or (resid 152...DD1 - 1513 - 153
42GLUGLUGLUGLU(chain D and (resid 1 through 151 or (resid 152...DD152154
43METMETPROPRO(chain D and (resid 1 through 151 or (resid 152...DD1 - 3573 - 359
44METMETPROPRO(chain D and (resid 1 through 151 or (resid 152...DD1 - 3573 - 359
45METMETPROPRO(chain D and (resid 1 through 151 or (resid 152...DD1 - 3573 - 359
46METMETPROPRO(chain D and (resid 1 through 151 or (resid 152...DD1 - 3573 - 359

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Components

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Protein , 1 types, 4 molecules ABCD

#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.: 4
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

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Non-polymers , 5 types, 35 molecules

#2: Chemical ChemComp-GDD / GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE


Mass: 605.341 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H25N5O16P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4O7P2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.72 Å3/Da / Density % sol: 66.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: magnesium formate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 49084 / % possible obs: 99.8 % / Redundancy: 11.1 % / CC1/2: 0.969 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.031 / Net I/σ(I): 26
Reflection shellResolution: 3→3.11 Å / Redundancy: 11 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4853 / CC1/2: 0.859 / Rpim(I) all: 0.366 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7D72

7d72


Resolution: 3→30.82 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2601 2442 5.01 %
Rwork0.2338 46332 -
obs0.2351 48774 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 158.26 Å2 / Biso mean: 58.6132 Å2 / Biso min: 25.14 Å2
Refinement stepCycle: final / Resolution: 3→30.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11002 0 178 11 11191
Biso mean--76.19 41.78 -
Num. residues----1442
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4947X-RAY DIFFRACTION15.949TORSIONAL
12B4947X-RAY DIFFRACTION15.949TORSIONAL
13C4947X-RAY DIFFRACTION15.949TORSIONAL
14D4947X-RAY DIFFRACTION15.949TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3-3.060.36611350.3623263197
3.06-3.130.37561220.32022738100
3.13-3.20.3071450.29622739100
3.2-3.280.34851280.30042708100
3.28-3.370.31221520.26952726100
3.37-3.470.2971580.29212716100
3.47-3.580.3151520.30042721100
3.58-3.710.29861280.25952725100
3.71-3.860.29331430.25882745100
3.86-4.030.28881500.2643260296
4.03-4.240.23261380.2223267198
4.25-4.510.25111720.19292724100
4.51-4.860.23261410.1763272899
4.86-5.340.23351380.18552759100
5.34-6.110.22751470.21612767100
6.11-7.680.23311400.21292809100
7.68-30.820.17981530.171282398
Refinement TLS params.Method: refined / Origin x: 31.5949 Å / Origin y: 0.3256 Å / Origin z: 92.4693 Å
111213212223313233
T0.2261 Å20.0098 Å2-0.0397 Å2-0.4143 Å2-0.0531 Å2--0.3136 Å2
L0.5609 °20.3721 °2-0.2456 °2-0.589 °2-0.283 °2--0.5605 °2
S-0.0102 Å °-0.1703 Å °-0.0814 Å °-0.058 Å °0.0104 Å °-0.0267 Å °-0.0934 Å °0.032 Å °-0.0029 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 366
2X-RAY DIFFRACTION1allA401 - 506
3X-RAY DIFFRACTION1allB1 - 506
4X-RAY DIFFRACTION1allC1 - 357
5X-RAY DIFFRACTION1allC402 - 504
6X-RAY DIFFRACTION1allD1 - 357
7X-RAY DIFFRACTION1allD501 - 505
8X-RAY DIFFRACTION1allS1 - 11

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