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- PDB-5jjt: Crystal structure of a type 5 serine/threonine protein phosphatas... -

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Basic information

Entry
Database: PDB / ID: 5jjt
TitleCrystal structure of a type 5 serine/threonine protein phosphatase from Arabidopsis thaliana
ComponentsSerine/threonine-protein phosphatase 5
KeywordsHYDROLASE / phosphatase
Function / homology
Function and homology information


negative regulation of chlorophyll biosynthetic process / red or far-red light signaling pathway / chloroplast-nucleus signaling pathway / tetrapyrrole binding / plasmodesma / nucleocytoplasmic transport / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / phosphoprotein phosphatase activity ...negative regulation of chlorophyll biosynthetic process / red or far-red light signaling pathway / chloroplast-nucleus signaling pathway / tetrapyrrole binding / plasmodesma / nucleocytoplasmic transport / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / phosphoprotein phosphatase activity / nuclear envelope / nuclear membrane / nuclear speck / endoplasmic reticulum membrane / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Tetratricopeptide repeat / PPP domain / PP5, C-terminal metallophosphatase domain / PPP5 TPR repeat region / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Tetratricopeptide repeat 1 / Tetratricopeptide repeat ...Tetratricopeptide repeat / PPP domain / PP5, C-terminal metallophosphatase domain / PPP5 TPR repeat region / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / 4-Layer Sandwich / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Serine/threonine-protein phosphatase 5
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.103 Å
AuthorsLi, H.M. / Pu, H.
CitationJournal: To Be Published
Title: Crystal structure of a type 5 serine/threonine protein phosphatase from Arabidopsis thaliana
Authors: Li, H.M. / Pu, H.
History
DepositionApr 25, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein phosphatase 5
B: Serine/threonine-protein phosphatase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,6918
Polymers108,3392
Non-polymers3526
Water13,872770
1
A: Serine/threonine-protein phosphatase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3454
Polymers54,1691
Non-polymers1763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint-36 kcal/mol
Surface area19830 Å2
MethodPISA
2
B: Serine/threonine-protein phosphatase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3454
Polymers54,1691
Non-polymers1763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint-36 kcal/mol
Surface area20090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.408, 102.705, 95.290
Angle α, β, γ (deg.)90.000, 95.570, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serine/threonine-protein phosphatase 5 / type 5 serine/threonine protein phosphatase


Mass: 54169.391 Da / Num. of mol.: 2 / Fragment: UNP residues 5-483 of isoform 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PAPP5, PP5, At2g42810, F7D19.19 / Production host: Escherichia coli (E. coli)
References: UniProt: Q84XU2, protein-serine/threonine phosphatase
#2: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: Ni
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 770 / 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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 0.1M HEPES pH7.2, 22.5% PEG 3350, 20% glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 55086 / % possible obs: 96.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 12.97
Reflection shellResolution: 2.1→2.18 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WAO

1wao


Resolution: 2.103→45.797 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 23.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2309 2756 5.06 %
Rwork0.1863 --
obs0.1886 54450 95.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.62 Å2 / Biso mean: 18.8251 Å2 / Biso min: 4.86 Å2
Refinement stepCycle: final / Resolution: 2.103→45.797 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7480 0 6 770 8256
Biso mean--24.68 23.33 -
Num. residues----950
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037719
X-RAY DIFFRACTIONf_angle_d0.70510447
X-RAY DIFFRACTIONf_chiral_restr0.0511129
X-RAY DIFFRACTIONf_plane_restr0.0031367
X-RAY DIFFRACTIONf_dihedral_angle_d11.7262865
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.103-2.13920.2951130.21592221233481
2.1392-2.17810.3021180.22422512263093
2.1781-2.220.28461380.21132545268394
2.22-2.26540.31331290.22152554268394
2.2654-2.31460.24091290.21232593272295
2.3146-2.36850.26061190.21292602272196
2.3685-2.42770.27681400.21622599273996
2.4277-2.49330.26491480.21292586273496
2.4933-2.56670.27531330.2112616274996
2.5667-2.64950.28811420.20592585272796
2.6495-2.74420.27751610.21132574273596
2.7442-2.85410.26541240.20312626275096
2.8541-2.98390.22251340.20022590272496
2.9839-3.14120.23471450.19382575272096
3.1412-3.3380.25361430.18692611275496
3.338-3.59560.23581460.17772640278697
3.5956-3.95730.18741360.17042677281397
3.9573-4.52940.18321490.15052639278898
4.5294-5.70490.17241620.15572656281897
5.7049-45.80770.19721470.16372693284097

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