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- PDB-4kyq: Structure of a product bound plant phosphatase -

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Basic information

Entry
Database: PDB / ID: 4kyq
TitleStructure of a product bound plant phosphatase
ComponentsPhosphoglucan phosphatase LSF2, chloroplastic
KeywordsHYDROLASE / SUGAR BINDING PROTEIN / Dual Specificity Phosphatase (DSP) fold / Glucan (starch) phosphatase / Carbohydrate/Sugar Binding / chloroplast
Function / homology
Function and homology information


carbohydrate phosphatase activity / sugar-phosphatase activity / starch catabolic process / starch binding / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / phosphoprotein phosphatase activity / chloroplast
Similarity search - Function
: / Laforin-like, dual specificity phosphatase domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine-specific protein phosphatases domain ...: / Laforin-like, dual specificity phosphatase domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / Phosphoglucan phosphatase LSF2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsMeekins, D.A. / Guo, H.-F. / Husodo, S. / Paasch, B.C. / Bridges, T.M. / Santelia, D. / Kotting, O. / Vander Kooi, C.W. / Gentry, M.S.
CitationJournal: Plant Cell / Year: 2013
Title: Structure of the Arabidopsis Glucan Phosphatase LIKE SEX FOUR2 Reveals a Unique Mechanism for Starch Dephosphorylation.
Authors: Meekins, D.A. / Guo, H.F. / Husodo, S. / Paasch, B.C. / Bridges, T.M. / Santelia, D. / Kotting, O. / Vander Kooi, C.W. / Gentry, M.S.
History
DepositionMay 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 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_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

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Assembly

Deposited unit
A: Phosphoglucan phosphatase LSF2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1352
Polymers23,9461
Non-polymers1891
Water2,900161
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.820, 99.582, 37.763
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Phosphoglucan phosphatase LSF2, chloroplastic / Phosphoglucan phosphatase like sex Four2 / Protein LIKE SEX4 2


Mass: 23946.178 Da / Num. of mol.: 1 / Fragment: UNP residues 79-282
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At3g10940, AT3G10940.1, F9F8.24, LSF2 / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q9SRK5, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.03 Å3/Da / Density % sol: 39.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 0.1M tri-sodium citrate, 16% 2-propanol, 31% PEG 4000, 2% glycerol, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 28, 2011
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.64→20 Å / Num. all: 24454 / Num. obs: 22033 / % possible obs: 90.1 % / Observed criterion σ(I): -3
Reflection shellResolution: 1.64→1.71 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.593 / Mean I/σ(I) obs: 2.25 / Num. unique all: 2061 / % possible all: 86.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3NME

3nme


Resolution: 1.64→19.63 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.658 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19909 1074 4.9 %RANDOM
Rwork0.15692 ---
obs0.15885 20833 89.24 %-
all-23345 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.766 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å2-0 Å20 Å2
2---0.23 Å2-0 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.64→19.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1672 0 13 161 1846
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021779
X-RAY DIFFRACTIONr_bond_other_d0.0010.021251
X-RAY DIFFRACTIONr_angle_refined_deg1.6781.972422
X-RAY DIFFRACTIONr_angle_other_deg0.93133042
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3765224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.623.59689
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.96615316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.181516
X-RAY DIFFRACTIONr_chiral_restr0.2570.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211999
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02369
LS refinement shellResolution: 1.64→1.685 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.352 74 -
Rwork0.274 1229 -
obs--79.4 %
Refinement TLS params.Method: refined / Origin x: 8.4422 Å / Origin y: -15.6792 Å / Origin z: 8.7293 Å
111213212223313233
T0.0261 Å20.0064 Å2-0.0018 Å2-0.0399 Å2-0.0033 Å2--0.0076 Å2
L0.8834 °2-0.2177 °2-0.0467 °2-1.8641 °2-0.061 °2--0.4782 °2
S0.0144 Å °-0.0213 Å °-0.0209 Å °-0.1307 Å °-0.0076 Å °-0.0777 Å °0.016 Å °-0.0152 Å °-0.0069 Å °

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