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- PDB-2icx: Crystal Structure of a Putative UDP-glucose Pyrophosphorylase fro... -

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Basic information

Entry
Database: PDB / ID: 2icx
TitleCrystal Structure of a Putative UDP-glucose Pyrophosphorylase from Arabidopsis Thaliana with Bound UTP
ComponentsProbable UTP-glucose-1-phosphate uridylyltransferase 2
KeywordsTRANSFERASE / At3g03250 / UTP / putative UDP-glucose pyrophosphorylase / Structural Genomics Functional Follow-up Study / Structural Genomics / Protein Structure Initiative / PSI / CESG / Center for Eukaryotic Structural Genomics
Function / homology
Function and homology information


callose deposition in cell wall / pollen tube / sucrose metabolic process / UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / pollen development / UDP-glucose metabolic process / cellular response to phosphate starvation / plasma membrane / cytosol
Similarity search - Function
UTP--glucose-1-phosphate uridylyltransferase / UDPGP family / UTP--glucose-1-phosphate uridylyltransferase / 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 ...UTP--glucose-1-phosphate uridylyltransferase / UDPGP family / UTP--glucose-1-phosphate uridylyltransferase / 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
URIDINE 5'-TRIPHOSPHATE / UTP--glucose-1-phosphate uridylyltransferase 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMcCoy, J.G. / Wesenberg, G.E. / Phillips Jr., G.N. / Bitto, E. / Bingman, C.A. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structure and Dynamics of UDP-Glucose Pyrophosphorylase from Arabidopsis thaliana with Bound UDP-Glucose and UTP.
Authors: McCoy, J.G. / Bitto, E. / Bingman, C.A. / Wesenberg, G.E. / Bannen, R.M. / Kondrashov, D.A. / Phillips Jr., G.N.
History
DepositionSep 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable UTP-glucose-1-phosphate uridylyltransferase 2
B: Probable UTP-glucose-1-phosphate uridylyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,5555
Polymers103,5082
Non-polymers1,0463
Water15,691871
1
A: Probable UTP-glucose-1-phosphate uridylyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3163
Polymers51,7541
Non-polymers5622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable UTP-glucose-1-phosphate uridylyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2382
Polymers51,7541
Non-polymers4841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)187.683, 59.679, 89.813
Angle α, β, γ (deg.)90.000, 100.380, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1088-

HOH

21A-1101-

HOH

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Components

#1: Protein Probable UTP-glucose-1-phosphate uridylyltransferase 2 / UDP-glucose pyrophosphorylase 2 / UDPGP 2 / UGPase 2


Mass: 51754.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At3g03250, T17B22.6 / Plasmid: PVP-17 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2)
References: UniProt: Q9M9P3, UTP-glucose-1-phosphate uridylyltransferase
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE / Uridine triphosphate


Mass: 484.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 871 / Source method: isolated from a natural source / Formula: H2O

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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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.3948.51
2
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop with micro-seeding
Details: Protein solution (10 mg/ml protein, 0.050 M sodium chloride, 0.0003 M TCEP, 0.005 M Tris PH 8.0) mixed in a 1:1 ratio with Well solution ( 28 % PEG 2K, 5% DMSO, 0.10 M MES/Acetate pH 5.5), ...Details: Protein solution (10 mg/ml protein, 0.050 M sodium chloride, 0.0003 M TCEP, 0.005 M Tris PH 8.0) mixed in a 1:1 ratio with Well solution ( 28 % PEG 2K, 5% DMSO, 0.10 M MES/Acetate pH 5.5), crystals soaked in well solution supplemented with 0.002 M UTP, vapor diffusion, hanging drop with micro-seeding, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: BRUKER PROTEUM-R / Detector: CCD / Date: May 2, 2006 / Details: MONTEL OPTICS
RadiationMonochromator: Graded Multilayer / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→70.481 Å / Num. obs: 83235 / % possible obs: 99.4 % / Redundancy: 14.3 % / Rmerge(I) obs: 0.0353 / Net I/σ(I): 23.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique all% possible all
1.85-1.95.090.31153.196377100
1.9-1.956.030.24693.985766100
1.95-26.850.19165.045239100
2-2.050.15726.064689100
2.05-2.10.13537.014237100
2.1-2.28.670.10788.77744799.8
2.2-2.310.10.078411.8609899
2.3-2.411.190.062714.71513798.4
2.4-2.50.048818.43431297.8
2.5-2.650.0422.21524797.3
2.65-2.850.030627.87556499.6
2.85-3.10.022536.515132100
3.1-3.450.017346.964899100
3.45-40.014358.54671100
4-5.050.01371.274211100
5.05-70.4810.01472.84420998.1

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Phasing

Phasing MRRfactor: 0.484 / Cor.coef. Fo:Fc: 0.398
Highest resolutionLowest resolution
Rotation3 Å70.48 Å
Translation3 Å70.48 Å

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Processing

Software
NameVersionClassificationNB
SAINTdata scaling
MOLREPphasing
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
SAINTdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z90

1z90


Resolution: 1.85→70.481 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.916 / WRfactor Rfree: 0.23 / WRfactor Rwork: 0.189 / SU B: 5.927 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.239 4158 4.996 %RANDOM
Rwork0.192 ---
obs0.195 83222 99.371 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 11.405 Å2
Baniso -1Baniso -2Baniso -3
1--0.363 Å20 Å2-0.235 Å2
2---0.398 Å20 Å2
3---0.676 Å2
Refinement stepCycle: LAST / Resolution: 1.85→70.481 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7132 0 62 871 8065
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0227333
X-RAY DIFFRACTIONr_angle_refined_deg1.9021.9889961
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9635918
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.00525.926297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.536151323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5971520
X-RAY DIFFRACTIONr_chiral_restr0.1060.21165
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025364
X-RAY DIFFRACTIONr_nbd_refined0.2080.23487
X-RAY DIFFRACTIONr_nbtor_refined0.3080.25020
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2764
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.237
X-RAY DIFFRACTIONr_mcbond_it0.8681.54705
X-RAY DIFFRACTIONr_mcangle_it1.29827453
X-RAY DIFFRACTIONr_scbond_it2.25332952
X-RAY DIFFRACTIONr_scangle_it3.4544.52503
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.8980.2863160.2345852616999.984
1.898-1.950.3262780.20756985976100
1.95-2.0070.242480.20255845832100
2.007-2.0680.2612840.19753885672100
2.068-2.1360.262730.1965255553199.946
2.136-2.2110.2652720.1885001529799.547
2.211-2.2940.2512840.1924831516499.051
2.294-2.3880.2152520.1854584491698.373
2.388-2.4940.2322170.1834449476597.922
2.494-2.6160.2092150.1924155450996.917
2.616-2.7570.2262230.1914068432999.122
2.757-2.9240.2582040.1943888409499.951
2.924-3.1260.2391760.1883673385099.974
3.126-3.3760.2231950.1934163611100
3.376-3.6980.2221600.1823150331199.97
3.698-4.1330.2161680.17428373005100
4.133-4.7710.21400.1582508264999.962
4.771-5.840.2281250.19121412266100
5.84-8.2420.295880.2271696178699.888
8.242-92.450.295400.305890101791.445

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