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- PDB-7obe: X-ray structure of the phosphatase PAPP5 from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 7obe
TitleX-ray structure of the phosphatase PAPP5 from Arabidopsis thaliana
ComponentsIsoform 2 of Serine/threonine-protein phosphatase 5
KeywordsSIGNALING PROTEIN / PHOSPHATASE / PP5 / ARABIDOPSIS THALIANA / HYDROLASE
Function / homology
Function and homology information


negative regulation of chlorophyll biosynthetic process / chloroplast-nucleus signaling pathway / red or far-red light signaling pathway / tetrapyrrole binding / plasmodesma / nucleocytoplasmic transport / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / phosphoprotein phosphatase activity / nuclear envelope ...negative regulation of chlorophyll biosynthetic process / chloroplast-nucleus signaling pathway / red or far-red light signaling pathway / tetrapyrrole binding / plasmodesma / nucleocytoplasmic transport / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / phosphoprotein phosphatase activity / nuclear envelope / nuclear membrane / nuclear speck / endoplasmic reticulum membrane / metal ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Tetratricopeptide repeat / PP5, C-terminal metallophosphatase domain / PPP domain / PPP5 TPR repeat region / : / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Tetratricopeptide repeat / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase ...Tetratricopeptide repeat / PP5, C-terminal metallophosphatase domain / PPP domain / PPP5 TPR repeat region / : / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Tetratricopeptide repeat / 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 / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
: / Serine/threonine-protein phosphatase 5
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
Authorsvon Horsten, S. / Essen, L.-O.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)ES152/10 Germany
CitationJournal: Front Plant Sci / Year: 2021
Title: Conformational Change of Tetratricopeptide Repeats Region Triggers Activation of Phytochrome-Associated Protein Phosphatase 5.
Authors: von Horsten, S. / Essen, L.O.
History
DepositionApr 22, 2021Deposition site: PDBE / Processing site: PDBE
SupersessionJun 9, 2021ID: 5OBL
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 2 of Serine/threonine-protein phosphatase 5
B: Isoform 2 of Serine/threonine-protein phosphatase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,3308
Polymers114,0392
Non-polymers2916
Water37821
1
A: Isoform 2 of Serine/threonine-protein phosphatase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1654
Polymers57,0201
Non-polymers1453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Isoform 2 of Serine/threonine-protein phosphatase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1654
Polymers57,0201
Non-polymers1453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.580, 103.010, 95.060
Angle α, β, γ (deg.)90.000, 95.564, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 9 through 112 or (resid 113...
d_2ens_1(chain "B" and (resid 9 through 143 or resid 145 through 483))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASPGLUA5 - 139
d_12ens_1ARGPHEA141 - 479
d_21ens_1ASPGLUB1 - 135
d_22ens_1ARGPHEB139 - 477

NCS oper: (Code: givenMatrix: (0.999951213004, 0.0096974183215, -0.00187927929471), (0.00965156524224, -0.999687961653, -0.023039674776), (-0.0021021182518, 0.0230204127527, -0.999732785146)Vector: - ...NCS oper: (Code: given
Matrix: (0.999951213004, 0.0096974183215, -0.00187927929471), (0.00965156524224, -0.999687961653, -0.023039674776), (-0.0021021182518, 0.0230204127527, -0.999732785146)
Vector: -26.0809794773, 65.4972965672, -51.6177844176)

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Components

#1: Protein Isoform 2 of Serine/threonine-protein phosphatase 5


Mass: 57019.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PAPP5, PP5, At2g42810, F7D19.19 / Plasmid: pCDF Duet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold (DE3)
References: UniProt: Q84XU2, protein-serine/threonine phosphatase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.2 Å3/Da / Density % sol: 44.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES, PH 7.0, 50 % PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 14, 2014
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 3→34.84 Å / Num. obs: 19742 / % possible obs: 99.06 % / Redundancy: 1.9 % / Biso Wilson estimate: 31.74 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 13.7
Reflection shellResolution: 3→3.1 Å / Rmerge(I) obs: 0.24 / Num. unique obs: 1982 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.18_3861refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WAO

1wao


Resolution: 3→34.84 Å / SU ML: 0.3614 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.3245
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2426 900 4.56 %
Rwork0.21 18838 -
obs0.2115 19738 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.67 Å2
Refinement stepCycle: LAST / Resolution: 3→34.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7597 0 6 21 7624
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037782
X-RAY DIFFRACTIONf_angle_d0.582410502
X-RAY DIFFRACTIONf_chiral_restr0.04221118
X-RAY DIFFRACTIONf_plane_restr0.0051379
X-RAY DIFFRACTIONf_dihedral_angle_d15.58061041
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.454248588219 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.190.35471350.29133159X-RAY DIFFRACTION99.61
3.19-3.430.28681800.25333120X-RAY DIFFRACTION99.64
3.43-3.780.23151350.21773136X-RAY DIFFRACTION99.51
3.78-4.320.22371350.19123169X-RAY DIFFRACTION99.07
4.32-5.450.22761800.18213073X-RAY DIFFRACTION98.58
5.45-34.840.19151350.17573181X-RAY DIFFRACTION98.28
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)
11.94395176398-0.1315792846610.3465731349660.9668634919770.2342237402743.545722506550.1628141486940.4514551392440.242382822436-0.4794925135630.00829481897983-0.08566197922650.1415556536490.0332636313412-0.1733666840180.2333589141660.0313526003362-0.01633325858480.242712525050.04922824664490.1799561449287.1764148725138.798225111-62.8695230503
22.20561948030.4975750378960.2906515144072.08491182443-0.5729915917425.09162525999-0.05097926179860.147351253338-0.516272419034-0.179159927011-0.140412059281-0.3764349971340.3736663283081.118646637340.1031947874810.3773616818390.0979625033187-0.06793078533310.435020234988-0.01012880820710.29004762964417.847872462527.5515663578-49.1482211427
32.36771217224-0.03153690078850.116826830572.46422933608-0.2175892254831.962596284310.238200142167-0.5476363644240.230046374330.89069120751-0.208804351326-0.340630447137-0.432553287880.394167677398-0.08785040371090.461535618256-0.0787339445360.01395558229710.407162954309-0.08174252821450.3106092588499.3658182455353.7522467122-19.2174394923
40.637844880973-0.837507035203-0.5939998448554.117238783470.1112279002860.6937059590410.123667044870.2882775813110.0733408829632-0.903084379979-0.1913611125-0.5636357450270.1290276122280.0221614492246-0.02282049248130.340372060992-0.03846948919530.0465894907590.321907706854-0.02189483610580.212127236893-16.213352929112.6651874414-31.1562721505
52.076461610721.10676412605-0.02407026342952.1445783535-0.126947653942.80960136730.1151491380960.2671873952580.1220897064960.004102362873420.08737999601140.066408689573-0.0926176137351-0.0936314402554-0.08830937647250.1868809614820.02533575293670.03024376266360.2028870334370.01652251245010.156376935403-2.455620896148.8057817177-38.9339957685
61.8086859304-0.2487622897311.065338714731.279144823391.133174151032.301033227890.367257316095-0.567625981071-0.5120901296041.08272162607-0.1404280677110.293370010780.977059995235-0.247774799584-0.1178192848410.528770975704-0.122125288421-0.0316559471080.3805305757060.04440148352030.251403746909-18.62015420128.965169397811.7190565368
71.12518547422-0.138326064806-0.008652786862841.328753577170.1196545866054.340298541550.04873233238560.04123985832750.1169402741130.0760306929183-0.0230926304159-0.3173189741230.2067497134090.6219844542450.01921811193710.302757758246-0.03482766267680.04426405524620.332604217491-0.0312513592040.2034050971-7.9899590407239.1919399873-2.01025459251
82.16901921706-0.648098442206-0.2224726962271.980277662590.3474906155421.66092041272-0.0373244104347-0.2215248471920.05536403645130.03722878660130.0702045761562-0.0849715448784-0.0576979893807-0.0431468861252-0.01543417277310.144925288986-0.00448088316026-0.02653171156280.191143480383-0.01662252751580.102260550887-28.0738858517.5156949194-11.6258362984
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 19 through 74 )AA19 - 7415 - 70
22chain 'A' and (resid 75 through 139 )AA75 - 13971 - 135
33chain 'A' and (resid 140 through 205 )AA140 - 205136 - 201
44chain 'B' and (resid 140 through 205 )BB140 - 205132 - 199
55chain 'A' and (resid 206 through 484 )AA206 - 484202 - 480
66chain 'B' and (resid 23 through 74 )BB23 - 7415 - 66
77chain 'B' and (resid 75 through 139)BB75 - 13967 - 131
88chain 'B' and (resid 206 through 483 )BB206 - 483200 - 477

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