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- PDB-2q47: Ensemble refinement of the protein crystal structure of a putativ... -

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Basic information

Entry
Database: PDB / ID: 2q47
TitleEnsemble refinement of the protein crystal structure of a putative phosphoprotein phosphatase from Arabidopsis thaliana gene At1g05000
ComponentsProbable tyrosine-protein phosphatase At1g05000
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Ensemble Refinement / Refinement Methodology Development / AT1G05000 / phosphoprotein phosphatase / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity / inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity / diphosphoinositol-polyphosphate diphosphatase / phosphatase activity / protein tyrosine phosphatase activity / cytoplasm
Similarity search - Function
Atypical dual-specificity phosphatase Siw14-like, plant and fungi / Atypical dual-specificity phosphatase Siw14-like / Tyrosine phosphatase family / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Protein-tyrosine phosphatase-like ...Atypical dual-specificity phosphatase Siw14-like, plant and fungi / Atypical dual-specificity phosphatase Siw14-like / Tyrosine phosphatase family / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Inositol diphosphatase DSP1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / Re-refinement using ensemble model / Resolution: 3.3 Å
AuthorsLevin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: 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.
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_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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable tyrosine-protein phosphatase At1g05000
B: Probable tyrosine-protein phosphatase At1g05000
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4646
Polymers35,0802
Non-polymers3844
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-82 kcal/mol
Surface area14530 Å2
MethodPISA, PQS
2
A: Probable tyrosine-protein phosphatase At1g05000
B: Probable tyrosine-protein phosphatase At1g05000
hetero molecules

A: Probable tyrosine-protein phosphatase At1g05000
B: Probable tyrosine-protein phosphatase At1g05000
hetero molecules

A: Probable tyrosine-protein phosphatase At1g05000
B: Probable tyrosine-protein phosphatase At1g05000
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,39218
Polymers105,2406
Non-polymers1,15312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Buried area13580 Å2
ΔGint-286 kcal/mol
Surface area37430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.483, 124.483, 124.483
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Number of models16

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Components

#1: Protein Probable tyrosine-protein phosphatase At1g05000


Mass: 17539.951 Da / Num. of mol.: 2 / Fragment: Residues 52-202
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: cv. Columbia / Description: pQE derivative / Gene: At1g05000, T7A14.14 / Plasmid: pVP-13 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9ZVN4, protein-tyrosine-phosphatase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.58 Å3/Da / Density % sol: 73.14 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 1XRI.

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Data collection

DetectorType: APS-1
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 1XRI

1xri


Resolution: 3.3→41.5 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 150641.594 / 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 1xri and the first data set in the deposited structure factor file for 1xri ...Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 1xri and the first data set in the deposited structure factor file for 1xri along with the R-free set defined therein. The coordinates were generated by an automated protocol from an initial model consisting of 16 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
Rfree0.234 937 9.5 %RANDOM
Rwork0.16 ---
obs0.16 9847 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.067 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso mean: 27.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 3.3→41.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2448 0 20 60 2528
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_d21.2
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it1.61.5
X-RAY DIFFRACTIONc_mcangle_it2.782
X-RAY DIFFRACTIONc_scbond_it1.922
X-RAY DIFFRACTIONc_scangle_it3.082.5
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 (%)
3.3-3.510.29616410.20.20214420.0231634160698.3
3.51-3.780.2381539.50.15114660.0191637161998.9
3.78-4.160.1981348.20.13414960.0171639163099.5
4.16-4.760.19217210.50.11714600.0151638163299.6
4.76-5.990.2531549.30.16914950.021657164999.5
5.99-41.490.2521609.40.19915510.021728171199
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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