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

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Basic information

Entry
Database: PDB / ID: 4kyr
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 profile. ...: / 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 profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
alpha-maltopentaose / alpha-maltohexaose / PHOSPHATE ION / Phosphoglucan phosphatase LSF2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoglucan phosphatase LSF2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6646
Polymers23,9301
Non-polymers3,7345
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.776, 92.776, 144.942
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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


Mass: 23930.111 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 79-282 / Mutation: C193S
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: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltohexaose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 990.860 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltohexaose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a2122h-1a_1-5]/1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltopentaose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 828.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltopentaose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1a_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}LINUCSPDB-CARE
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 3.76 Å3/Da / Density % sol: 67.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 25mM maltohexaose, 0.1M di-ammonium hydrogen phosphate, 17% 2-propanol, 31% PEG 4000, pH 5.7, 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: Mar 19, 2012
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 17059 / Num. obs: 16172 / % possible obs: 94.8 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 2.17 / Num. unique all: 1453 / % possible all: 87.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.53 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / SU B: 10.064 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22858 826 5.1 %RANDOM
Rwork0.17376 ---
obs0.17634 15288 94.4 %-
all-16195 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.402 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20.2 Å20 Å2
2--0.2 Å20 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1682 0 251 87 2020
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191995
X-RAY DIFFRACTIONr_bond_other_d0.0010.021776
X-RAY DIFFRACTIONr_angle_refined_deg2.0782.1112736
X-RAY DIFFRACTIONr_angle_other_deg1.40334068
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1875209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.38123.44887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.05715302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.691516
X-RAY DIFFRACTIONr_chiral_restr0.1970.2351
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211962
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02406
LS refinement shellResolution: 2.3→2.357 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.325 67 -
Rwork0.245 973 -
obs--85.39 %
Refinement TLS params.Method: refined / Origin x: 4.4459 Å / Origin y: 37.8325 Å / Origin z: -3.2914 Å
111213212223313233
T0.0278 Å20.0004 Å2-0.0021 Å2-0.0519 Å2-0.004 Å2--0.0063 Å2
L0.613 °2-0.0361 °20.2794 °2-0.1952 °2-0.0081 °2--0.2682 °2
S0.0208 Å °0.0453 Å °-0.0572 Å °-0.0083 Å °0.0014 Å °0.0162 Å °0.0067 Å °0.0297 Å °-0.0222 Å °

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