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- PDB-2h39: Crystal Structure of an ADP-Glucose Phosphorylase from Arabidopsi... -

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Basic information

Entry
Database: PDB / ID: 2h39
TitleCrystal Structure of an ADP-Glucose Phosphorylase from Arabidopsis thaliana with bound ADP-Glucose
ComponentsProbable galactose-1-phosphate uridyl transferase
KeywordsTRANSFERASE / At5g18200 / ADP-GLUCOSE / GALT-LIKE / STRUCTURAL GENOMICS FUNCTIONAL FOLLOW-UP STUDY / PROTEIN STRUCTURE INITIATIVE / PSI / CENTER FOR EUKARYOTIC STRUCTURAL GENOMICS / CESG
Function / homology
Function and homology information


ribose-5-phosphate adenylyltransferase activity / positive regulation of cellular response to phosphate starvation / UDP-glucose:hexose-1-phosphate uridylyltransferase activity / galactose catabolic process via UDP-galactose / nucleotidyltransferase activity / ADP binding / glucose metabolic process / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / carbohydrate metabolic process / zinc ion binding
Similarity search - Function
Galactose-1-phosphate uridyl transferase, N-terminal / Galactose-1-phosphate uridyl transferase, C-terminal / Galactose-1-phosphate uridyl transferase, N-terminal domain / Galactose-1-phosphate uridyl transferase, C-terminal domain / Galactose-1-phosphate uridyl transferase, class I / HIT-like / HIT family, subunit A / HIT-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE-GLUCOSE / ADP-glucose phosphorylase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsMcCoy, J.G. / Wesenberg, G.E. / Phillips Jr., G.N. / Bitto, E. / Bingman, C.A. / Center for Eukaryotic Structural Genomics (CESG)
Citation
Journal: To be Published
Title: Crystal Structure of an ADP-Glucose Phosphorylase from Arabidopsis thaliana with bound ADP-Glucose
Authors: McCoy, J.G. / Wesenberg, G.E. / Phillips Jr., G.N. / Bitto, E. / Bingman, C.A.
#1: Journal: Biochemistry / Year: 2006
Title: Structure and Mechanism of an ADP-Glucose Phosphorylase from Arabidopsis thaliana
Authors: McCoy, J.G. / Arabshahi, A. / Bitto, E. / Bingman, C.A. / Ruzicka, F.J. / Frey, P.A. / Phillips Jr., G.N.
History
DepositionMay 22, 2006Deposition site: RCSB / Processing site: RCSB
SupersessionJun 13, 2006ID: 2GDK
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 25, 2018Group: Data collection / Category: diffrn / diffrn_radiation / diffrn_source
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 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

Downloads & links

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Assembly

Deposited unit
A: Probable galactose-1-phosphate uridyl transferase
B: Probable galactose-1-phosphate uridyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,45510
Polymers77,9442
Non-polymers1,5118
Water6,684371
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8330 Å2
ΔGint-81 kcal/mol
Surface area23200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.318, 95.454, 110.504
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is a dimer. There is 1 biological unit in the asymmetric unit (chains A & B).

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Components

#1: Protein Probable galactose-1-phosphate uridyl transferase / Gal-1-P uridylyltransferase / UDP-glucose-hexose-1-phosphate uridylyltransferase


Mass: 38972.062 Da / Num. of mol.: 2 / Mutation: H186G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g18200 / Plasmid: PVP-16 / Production host: Escherichia coli (E. coli) / Strain (production host): BL834(DE3) P(RARE)
References: UniProt: Q9FK51, UDP-glucose-hexose-1-phosphate uridylyltransferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ADQ / ADENOSINE-5'-DIPHOSPHATE-GLUCOSE / ADENOSINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 589.342 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H25N5O15P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / 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

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10 MG/ML PROTEIN, 20% PEG 2000, 0.2M SODIUM CHLORIDE, 0.10M MES-ACETATE, vapor diffusion, hanging drop, temperature 293K

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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: Sep 10, 2005 / Details: MONTEL OPTICS
RadiationMonochromator: Graded Multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.23→47.73 Å / Num. obs: 32389 / % possible obs: 100 % / Redundancy: 11.78 % / Rmerge(I) obs: 0.1912 / Net I/σ(I): 11.28
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique all% possible all
2.23-2.257.340.67562.9284099.9
2.25-2.37.550.56713.541969100
2.3-2.357.890.55823.851816100
2.35-2.48.10.54284165799.9
2.4-2.58.540.49624.472954100
2.5-2.69.180.44995.112514100
2.6-2.79.760.38146.342170100
2.7-2.810.460.33997.341869100
2.8-2.9511.40.29438.82336100
2.95-3.112.720.250411.071936100
3.1-3.314.020.217913.552065100
3.3-3.5514.110.178216.191957100
3.55-3.8513.590.165518.061755100
3.85-4.2514.580.127820.971622100
4.25-4.915.850.110323.231663100
4.9-6.2519.920.111324.711639100
6.25-47.7318.070.09326.04162799.6

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Phasing

Phasing MRRfactor: 0.416 / Cor.coef. Fo:Fc: 0.593
Highest resolutionLowest resolution
Rotation3 Å72.23 Å
Translation3 Å72.23 Å

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Processing

Software
NameVersionClassificationNB
SAINTdata scaling
MOLREPphasing
REFMAC5.2.0005refinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 1Z84

1z84


Resolution: 2.23→47.727 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.896 / WRfactor Rfree: 0.223 / WRfactor Rwork: 0.17 / SU B: 6.285 / SU ML: 0.157 / ESU R: 0.304 / ESU R Free: 0.231 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2434 1639 5.074 %
Rwork0.1761 --
all0.179 --
obs-32302 99.91 %
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: 18.776 Å2
Baniso -1Baniso -2Baniso -3
1-0.031 Å20 Å20 Å2
2---0.031 Å20 Å2
3---0.001 Å2
Refinement stepCycle: LAST / Resolution: 2.23→47.727 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4904 0 82 371 5357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0225128
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.9736975
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.735615
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.76124.081223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84215829
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.7561524
X-RAY DIFFRACTIONr_chiral_restr0.1110.2773
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023858
X-RAY DIFFRACTIONr_nbd_refined0.2010.22511
X-RAY DIFFRACTIONr_nbtor_refined0.310.23447
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2411
X-RAY DIFFRACTIONr_metal_ion_refined0.1780.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2870.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.27
X-RAY DIFFRACTIONr_mcbond_it1.51623212
X-RAY DIFFRACTIONr_mcangle_it2.7345082
X-RAY DIFFRACTIONr_scbond_it3.72282189
X-RAY DIFFRACTIONr_scangle_it2.78431893
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)
2.23-2.2880.3191170.21822250.223234999.702
2.288-2.3510.3011180.221690.205228999.913
2.351-2.4180.2681150.20521010.208221899.91
2.418-2.4930.31100.20620360.21214799.953
2.493-2.5740.31060.19820400.2032146100
2.574-2.6640.2991160.19219170.1982033100
2.664-2.7650.316930.18618750.191197099.898
2.765-2.8770.2551010.1917820.194188499.947
2.877-3.0040.228980.18817270.191825100
3.004-3.1510.25950.1716450.1741740100
3.151-3.320.259850.17215910.1761676100
3.32-3.520.2730.15815160.16159099.937
3.52-3.7620.208760.15314090.156148799.866
3.762-4.0610.201620.1513390.152140399.857
4.061-4.4460.196590.14612170.1481276100
4.446-4.9650.199580.13111170.135117799.83
4.965-5.7230.234610.1629980.1661059100
5.723-6.9840.223490.1888470.19896100
6.984-9.7730.165330.1726850.17271999.861
9.773-47.7270.183140.2324270.2344798.658

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