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- PDB-4pyh: Phospho-glucan bound structure of starch phosphatase Starch EXces... -

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Basic information

Entry
Database: PDB / ID: 4pyh
TitlePhospho-glucan bound structure of starch phosphatase Starch EXcess4 reveals the mechanism for C6-specificty
ComponentsPhosphoglucan phosphatase DSP4, chloroplastic
KeywordsHYDROLASE / starch phosphatase / chloroplast / Dual-Specificity Phosphatase / Carbohydrate Binding
Function / homology
Function and homology information


amylopectin binding / carbohydrate phosphatase activity / starch metabolic process / starch catabolic process / protein tyrosine/serine/threonine phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / chloroplast stroma / polysaccharide binding / dephosphorylation / chloroplast
Similarity search - Function
Laforin-like, dual specificity phosphatase domain / AMP-activated protein kinase, glycogen-binding domain / Glycogen recognition site of AMP-activated protein kinase / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A ...Laforin-like, dual specificity phosphatase domain / AMP-activated protein kinase, glycogen-binding domain / Glycogen recognition site of AMP-activated protein kinase / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-maltohexaose / PHOSPHATE ION / Phosphoglucan phosphatase DSP4, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMeekins, D.A. / Vander Kooi, C.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Phosphoglucan-bound structure of starch phosphatase Starch Excess4 reveals the mechanism for C6 specificity.
Authors: Meekins, D.A. / Raththagala, M. / Husodo, S. / White, C.J. / Guo, H.F. / Kotting, O. / Vander Kooi, C.W. / Gentry, M.S.
History
DepositionMar 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
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 / pdbx_struct_conn_angle / 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_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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 DSP4, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7155
Polymers33,5121
Non-polymers1,2024
Water6,377354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.475, 77.893, 117.213
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Phosphoglucan phosphatase DSP4, chloroplastic / AtPTPKIS1 / Dual specificity protein phosphatase 4 / Protein STARCH-EXCESS 4 / AtSEX4


Mass: 33512.305 Da / Num. of mol.: 1 / Fragment: UNP residues 90-379 / Mutation: C198S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DSP4, PTPKIS1, SEX4, At3g52180, F4F15.290 / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q9FEB5, 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.: 1
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

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Non-polymers , 4 types, 357 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 2.28 Å3/Da / Density % sol: 46.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M magnesium chloride, 20% PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 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: 1.65→20 Å / Num. all: 37915 / Num. obs: 36096 / % possible obs: 95.2 % / Observed criterion σ(I): -3
Reflection shellResolution: 1.65→1.71 Å / % possible all: 91

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX1.7.3-928model building
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7.3-928phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NME

3nme


Resolution: 1.65→19.43 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.138 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21763 1807 5 %RANDOM
Rwork0.17706 ---
obs0.17909 34257 --
all-36064 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.514 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.65→19.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2343 0 79 354 2776
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192555
X-RAY DIFFRACTIONr_bond_other_d0.0010.022420
X-RAY DIFFRACTIONr_angle_refined_deg1.5172.0023452
X-RAY DIFFRACTIONr_angle_other_deg1.38735571
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6265309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.06823.482112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.95415450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0451519
X-RAY DIFFRACTIONr_chiral_restr0.1250.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212784
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02565
X-RAY DIFFRACTIONr_mcbond_it1.1351.6051209
X-RAY DIFFRACTIONr_mcbond_other1.1241.6021208
X-RAY DIFFRACTIONr_mcangle_it1.8652.4011521
X-RAY DIFFRACTIONr_mcangle_other1.8672.4041522
X-RAY DIFFRACTIONr_scbond_it1.611.8031346
X-RAY DIFFRACTIONr_scbond_other1.611.8031346
X-RAY DIFFRACTIONr_scangle_other2.5772.6281930
X-RAY DIFFRACTIONr_long_range_B_refined5.04614.1143118
X-RAY DIFFRACTIONr_long_range_B_other4.63513.2772916
LS refinement shellResolution: 1.649→1.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 124 -
Rwork0.234 2317 -
obs--89.12 %
Refinement TLS params.Method: refined / Origin x: 11.104 Å / Origin y: -1.366 Å / Origin z: -1.56 Å
111213212223313233
T0.0101 Å2-0.0037 Å20.0006 Å2-0.0081 Å20.0012 Å2--0.0076 Å2
L0.64 °20.1082 °20.492 °2-0.8717 °2-0.2264 °2--1.7654 °2
S-0.0135 Å °0.0551 Å °0.0335 Å °-0.0884 Å °0.0155 Å °-0.0009 Å °0.0523 Å °-0.0082 Å °-0.0019 Å °

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