[English] 日本語
Yorodumi
- PDB-7obe: X-ray structure of the phosphatase PAPP5 from Arabidopsis thaliana -

+
Open data


ID or keywords:

Loading...

-
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 activity / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity ...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 activity / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / calmodulin-dependent protein phosphatase activity / myosin 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more