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- PDB-2q4l: Ensemble refinement of the crystal structure of GALT-like protein... -

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Basic information

Entry
Database: PDB / ID: 2q4l
TitleEnsemble refinement of the crystal structure of GALT-like protein from Arabidopsis thaliana At5g18200
ComponentsProbable galactose-1-phosphate uridyl transferase
KeywordsTRANSFERASE / Ensemble Refinement / Refinement Methodology Development / GALT / AT5G18200 / Structural Genomics / 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 metabolic process / 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
ADP-glucose phosphorylase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / Re-refinement using ensemble model / Resolution: 2.3 Å
AuthorsLevin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
Citation
Journal: Structure / Year: 2007
Title: Ensemble refinement of protein crystal structures: validation and application.
Authors: Levin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips, G.N.
#1: Journal: Biochemistry / Year: 2006
Title: ? Structure and Mechanism of an ADP-Glucose Phosphorylase from
Authors: McCoy, J.G. / Arabshahi, A. / Bitto, E. / Bingman, C.A. / Ruzicka, F.J. / Frey, P.A. / Phillips Jr., G.N.
History
DepositionMay 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 10, 2011Group: Other
Revision 1.4Aug 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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)78,3686
Polymers78,1062
Non-polymers2624
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-34 kcal/mol
Surface area23700 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)59.984, 95.535, 110.522
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Number of models4

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Components

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


Mass: 39053.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: cv. Columbia / Gene: At5g18200, MRG7_16 / Plasmid: PVP13 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.28 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 1ZWJ.

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT2data extraction
CNS1.1phasing
RefinementMethod to determine structure: Re-refinement using ensemble model
Starting model: PDB entry 1ZWJ

1zwj


Resolution: 2.3→27.26 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 357092.375 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: maximum likelihood using amplitudes
Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 1zwj and the first data set in the deposited structure factor file for 1zwj ...Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 1zwj and the first data set in the deposited structure factor file for 1zwj along with the R-free set defined therein. The coordinates were generated by an automated protocol from an initial model consisting of 4 identical copies of the protein and non-water hetero-atoms assigned fractional occupancies adding up to one, and a single copy of the solvent molecules. Refinement was carried out with all the conformers present simultaneously and with the potential energy terms corresponding to interactions between the different conformers excluded. The helix and sheet records were calculated using coordinates from the first conformer only. The structure visualization program PYMOL is well-suited for directly viewing the ensemble model presented in this PDB file.
RfactorNum. reflection% reflectionSelection details
Rfree0.27 2581 10 %RANDOM
Rwork0.19 ---
obs0.19 25917 89.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.88 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso mean: 43.9 Å2
Baniso -1Baniso -2Baniso -3
1-6.25 Å20 Å20 Å2
2--6.71 Å20 Å2
3----12.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.3→27.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4756 0 4 225 4985
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.312
X-RAY DIFFRACTIONc_scbond_it1.852
X-RAY DIFFRACTIONc_scangle_it2.462.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.3-2.450.38134210.20.27430210.0214712336371.4
2.45-2.630.3043839.70.22235840.0164761396783.3
2.63-2.90.3234009.40.21638750.0164750427590
2.9-3.320.32646910.30.21741050.0154791457495.5
3.32-4.180.25449410.40.18142680.0114825476298.7
4.18-27.260.2294939.90.16544830.015011497699.3
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.param

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