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- PDB-6ae9: X-ray structure of the photosystem II phosphatase PBCP -

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Basic information

Entry
Database: PDB / ID: 6ae9
TitleX-ray structure of the photosystem II phosphatase PBCP
ComponentsProbable protein phosphatase 2C 1Probability
KeywordsHYDROLASE / PP2C phosphatase / photosystem II phosphatase
Function / homology
Function and homology information


thylakoid membrane organization / protein serine/threonine phosphatase activity => GO:0004722 / protein serine/threonine phosphatase activity => GO:0004722 / peptidyl-threonine dephosphorylation / cellular response to light stimulus / chloroplast stroma / protein-serine/threonine phosphatase / metal ion binding
Similarity search - Function
Protein phosphatase 2C / Stage II sporulation protein E (SpoIIE) / Sigma factor PP2C-like phosphatases / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily
Similarity search - Domain/homology
: / PHOSPHATE ION / Chem-POG / Probable protein phosphatase 2C 1
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsLiu, X.Y. / Chai, J.C. / Ou, X.M. / Liu, Z.F.
Funding support China, 4items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2017YFA0503702 China
Chinese Academy of SciencesXDB08020302 China
Chinese Academy of SciencesQYZDB-SSW-SMC005 China
National Natural Science Foundation of China31670749 China
CitationJournal: Mol Plant / Year: 2019
Title: Structural Insights into Substrate Selectivity, Catalytic Mechanism, and Redox Regulation of Rice Photosystem II Core Phosphatase.
Authors: Liu, X. / Chai, J. / Ou, X. / Li, M. / Liu, Z.
History
DepositionAug 3, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable protein phosphatase 2C 1
B: Probable protein phosphatase 2C 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,13115
Polymers56,4122
Non-polymers1,71913
Water10,737596
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-94 kcal/mol
Surface area21720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.407, 166.407, 46.983
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-796-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Probable protein phosphatase 2C 1 / Probability / OsPP2C01


Mass: 28205.980 Da / Num. of mol.: 2 / Mutation: D283N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: Os01g0164600, LOC_Os01g07090, B1189A09.48, OsJ_000491, P0701D05.3
Production host: Escherichia coli (E. coli)
References: UniProt: Q942P9, protein-serine/threonine phosphatase

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Non-polymers , 5 types, 609 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-POG / (20S)-2,5,8,11,14,17-HEXAMETHYL-3,6,9,12,15,18-HEXAOXAHENICOSANE-1,20-DIOL / POLYPROPYLENE GLYCOL / HEPTAPROPYLENE GLYCOL / Polypropylene glycol


Mass: 424.569 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H44O8
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 596 / 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: 2.3 Å3/Da / Density % sol: 46.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.3 M MgCl2, 0.1 M Tris-HCl, pH 8.1, 29% PEG4000, 5% v/v Jeffamine M-600

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.47→30 Å / Num. obs: 81886 / % possible obs: 99.7 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 26.3
Reflection shellResolution: 1.47→1.52 Å / Rmerge(I) obs: 0.397 / Num. unique obs: 7948

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data scaling
PHASERphasing
ARP/wARPmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J82

2j82


Resolution: 1.47→27.7 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 17.5
RfactorNum. reflection% reflection
Rfree0.1789 4123 5.04 %
Rwork0.1596 --
obs0.1606 81882 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.47→27.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3818 0 101 596 4515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054007
X-RAY DIFFRACTIONf_angle_d0.8255414
X-RAY DIFFRACTIONf_dihedral_angle_d6.152275
X-RAY DIFFRACTIONf_chiral_restr0.077628
X-RAY DIFFRACTIONf_plane_restr0.004686
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.472-1.48930.2491290.20812575X-RAY DIFFRACTION97
1.4893-1.50750.20861540.19452685X-RAY DIFFRACTION100
1.5075-1.52650.17971300.18412651X-RAY DIFFRACTION99
1.5265-1.54660.20031690.18632671X-RAY DIFFRACTION100
1.5466-1.56780.22291370.18182693X-RAY DIFFRACTION99
1.5678-1.59020.2321190.17852680X-RAY DIFFRACTION100
1.5902-1.61390.20551240.1732724X-RAY DIFFRACTION100
1.6139-1.63920.18981250.1722685X-RAY DIFFRACTION99
1.6392-1.6660.21021610.17492676X-RAY DIFFRACTION100
1.666-1.69480.20761480.17652668X-RAY DIFFRACTION99
1.6948-1.72560.20451330.16792663X-RAY DIFFRACTION100
1.7256-1.75870.18411580.17222691X-RAY DIFFRACTION100
1.7587-1.79460.16741650.1672684X-RAY DIFFRACTION100
1.7946-1.83370.20261400.16792717X-RAY DIFFRACTION100
1.8337-1.87630.21211210.1662729X-RAY DIFFRACTION100
1.8763-1.92320.18611500.16112625X-RAY DIFFRACTION100
1.9232-1.97520.19321350.16422737X-RAY DIFFRACTION100
1.9752-2.03330.17291690.15512681X-RAY DIFFRACTION100
2.0333-2.09890.16571540.15742655X-RAY DIFFRACTION100
2.0989-2.17390.17461190.14892674X-RAY DIFFRACTION100
2.1739-2.26090.20131510.15452723X-RAY DIFFRACTION100
2.2609-2.36370.16321620.16222656X-RAY DIFFRACTION100
2.3637-2.48830.17241220.16242728X-RAY DIFFRACTION100
2.4883-2.64410.21131270.16242693X-RAY DIFFRACTION100
2.6441-2.8480.15721450.16492687X-RAY DIFFRACTION100
2.848-3.13430.17121470.16262702X-RAY DIFFRACTION100
3.1343-3.5870.15571520.14732690X-RAY DIFFRACTION100
3.587-4.51610.17081390.13572677X-RAY DIFFRACTION100
4.5161-27.73940.1661380.15822639X-RAY DIFFRACTION98

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