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- PDB-3nme: Structure of a plant phosphatase -

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Basic information

Entry
Database: PDB / ID: 3nme
TitleStructure of a plant phosphatase
ComponentsSEX4 glucan phosphatase
KeywordsHYDROLASE / Phosphatase / dual specificity phosphatase / Carbohydrate binding
Function / homology
Function and homology information


: / amylopectin binding / carbohydrate phosphatase activity / starch metabolic process / starch catabolic process / starch binding / protein tyrosine/serine/threonine phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / chloroplast stroma / polysaccharide binding ...: / amylopectin binding / carbohydrate phosphatase activity / starch metabolic process / starch catabolic process / starch binding / protein tyrosine/serine/threonine phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / chloroplast stroma / polysaccharide binding / dephosphorylation / chloroplast / circadian rhythm
Similarity search - Function
Phosphoglucan phosphatase DSP4 / 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 ...Phosphoglucan phosphatase DSP4 / 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
PHOSPHATE ION / Phosphoglucan phosphatase DSP4, chloroplastic / Phosphoglucan phosphatase DSP4, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsVander Kooi, C.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural basis for the glucan phosphatase activity of Starch Excess4.
Authors: Vander Kooi, C.W. / Taylor, A.O. / Pace, R.M. / Meekins, D.A. / Guo, H.F. / Kim, Y. / Gentry, M.S.
History
DepositionJun 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SEX4 glucan phosphatase
B: SEX4 glucan phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7554
Polymers67,5652
Non-polymers1902
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-22 kcal/mol
Surface area27030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.408, 73.943, 162.382
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SEX4 glucan phosphatase / PTPKIS1 protein


Mass: 33782.531 Da / Num. of mol.: 2 / Fragment: UNP residues 90-379 / Mutation: C198S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At3g52180 / Plasmid: pet28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q944A8, UniProt: Q9FEB5*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.64 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.4 M lithium citrate, 24% PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9792 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 9, 2010
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 26875 / Num. obs: 26660 / % possible obs: 99.2 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 2.04 / % possible all: 94.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→19.86 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.911 / SU B: 18.353 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24959 2000 7.5 %RANDOM
Rwork0.19854 ---
obs0.20234 24660 100 %-
all-26660 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.418 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2---0.29 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4638 0 10 196 4844
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0224744
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.991.9716408
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7945577
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89323.636220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.96315857
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4141536
X-RAY DIFFRACTIONr_chiral_restr0.0640.2700
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213564
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2251.52872
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.45624643
X-RAY DIFFRACTIONr_scbond_it0.87931872
X-RAY DIFFRACTIONr_scangle_it1.3694.51765
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.404→2.465 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 122 -
Rwork0.227 1502 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.2043-0.0316-0.38884.25670.27154.96680.15520.09180.2501-0.3628-0.0735-0.2478-0.19920.5011-0.08170.05810.00510.080.21950.01610.14374.55752.201101.235
21.2220.4254-0.94372.6330.05673.3782-0.0626-0.0035-0.149-0.15350.0459-0.01160.25940.13170.01670.03570.018-0.00540.2067-0.02010.1779-3.48343.192110.778
33.8150.04571.60510.3412-0.43381.7626-0.00820.0330.22930.0018-0.015-0.0077-0.11560.07880.02310.0692-0.01090.00780.1222-0.0210.23239.96840.011131.328
45.9826-0.43381.79442.0409-0.65492.660.04230.0962-0.09080.0703-0.015-0.1762-0.0149-0.0004-0.02730.0997-0.02640.01960.11140.00260.1715.5735.567134.423
51.6553-1.051-0.6882.00390.7310.18690.06290.11240.1274-0.1787-0.0280.0972-0.0725-0.0827-0.03490.12720.007-0.0210.31030.00580.23152.22631.799128.964
62.5611-0.2999-1.05069.45060.31161.36390.0896-0.0285-0.34550.5444-0.43920.50690.3758-0.20490.34960.2015-0.06520.07560.2484-0.00330.1814-13.62943.024120.796
72.50760.0737-0.02152.5715-0.39083.15280.0269-0.03960.26180.0726-0.0398-0.357-0.22650.41370.01290.0184-0.0281-0.01370.2306-0.0220.203427.0624.563111.505
81.89810.28880.29930.83980.41482.5962-0.02290.05320.007-0.0701-0.0140.1479-0.0907-0.00760.03690.08490.0132-0.00350.20.01630.177816.21518.015103.522
90.55890.7568-0.14976.474-3.84773.8814-0.04970.0547-0.0378-0.0908-0.0109-0.4454-0.13250.08940.06060.07630.026-0.01050.1952-0.04160.147715.6731.23183.092
102.25921.563-0.42324.9992-2.12376.62860.0524-0.20290.1790.39940.0688-0.0332-0.4353-0.0882-0.12120.11530.0496-0.0280.1653-0.0410.065712.13737.31880.527
111.51660.1982-1.992312.9188-1.47242.57860.0090.2844-0.0753-1.02640.12420.50330.2133-0.4515-0.13320.15070.0204-0.18510.36590.04090.30284.68120.8487.322
1230.56263.63574.3834.79770.42547.5562-0.6060.9798-1.1358-0.46730.4982-0.31120.36090.17240.10780.15860.03210.03390.1299-0.03340.139219.0085.49695.624
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A90 - 166
2X-RAY DIFFRACTION2A167 - 240
3X-RAY DIFFRACTION3A241 - 285
4X-RAY DIFFRACTION4A286 - 321
5X-RAY DIFFRACTION5A322 - 347
6X-RAY DIFFRACTION6A348 - 378
7X-RAY DIFFRACTION7B90 - 166
8X-RAY DIFFRACTION8B167 - 235
9X-RAY DIFFRACTION9B236 - 288
10X-RAY DIFFRACTION10B289 - 323
11X-RAY DIFFRACTION11B324 - 359
12X-RAY DIFFRACTION12B360 - 378

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