[English] 日本語
Yorodumi
- PDB-3p86: Crystal structure of CTR1 kinase domain mutant D676N in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3p86
TitleCrystal structure of CTR1 kinase domain mutant D676N in complex with staurosporine
ComponentsSerine/threonine-protein kinase CTR1
KeywordsTRANSFERASE / kinase / ETR1 / ERS1 / ETR2 / Phosphorylation
Function / homology
Function and homology information


regulation of post-embryonic root development / regulation of timing of transition from vegetative to reproductive phase / negative regulation of ethylene-activated signaling pathway / sugar mediated signaling pathway / gibberellin biosynthetic process / response to ethylene / regulation of stem cell division / ethylene-activated signaling pathway / response to sucrose / response to fructose ...regulation of post-embryonic root development / regulation of timing of transition from vegetative to reproductive phase / negative regulation of ethylene-activated signaling pathway / sugar mediated signaling pathway / gibberellin biosynthetic process / response to ethylene / regulation of stem cell division / ethylene-activated signaling pathway / response to sucrose / response to fructose / protein serine/threonine/tyrosine kinase activity / protein autophosphorylation / response to hypoxia / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / ATP binding
Similarity search - Function
Ethylene-responsive protein kinase Le-CTR1 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain ...Ethylene-responsive protein kinase Le-CTR1 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
STAUROSPORINE / Serine/threonine-protein kinase CTR1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.496 Å
AuthorsMayerhofer, H. / Panneerselvam, S. / Mueller-Dieckmann, J.
CitationJournal: J. Mol. Biol. / Year: 2012
Title: Protein kinase domain of CTR1 from Arabidopsis thaliana promotes ethylene receptor cross talk.
Authors: Mayerhofer, H. / Panneerselvam, S. / Mueller-Dieckmann, J.
History
DepositionOct 13, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / citation
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Nov 1, 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 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine/threonine-protein kinase CTR1
B: Serine/threonine-protein kinase CTR1
A: STAUROSPORINE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9033
Polymers70,4372
Non-polymers4671
Water1,09961
1
A: Serine/threonine-protein kinase CTR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6852
Polymers35,2181
Non-polymers4671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serine/threonine-protein kinase CTR1


Theoretical massNumber of molelcules
Total (without water)35,2181
Polymers35,2181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)122.334, 122.334, 95.011
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

-
Components

#1: Protein Serine/threonine-protein kinase CTR1


Mass: 35218.469 Da / Num. of mol.: 2 / Fragment: Kinase domain (UNP RESIDUES 540-821) / Mutation: D676N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g03730, CTR1, F17C15_150 / Plasmid: pETM11/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q05609, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-STU / STAUROSPORINE / Staurosporine


Mass: 466.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H26N4O3 / Comment: anticancer, antifungal, antibiotic, alkaloid*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.25 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 1.0M Na/K phosphate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 30, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.496→44.284 Å / Num. obs: 25665 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.1 % / Biso Wilson estimate: 47.1 Å2
Reflection shellResolution: 2.5→2.64 Å / Rmerge(I) obs: 0.833 / Mean I/σ(I) obs: 2.39 / Num. unique all: 52905 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
EDNAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C4C

3c4c


Resolution: 2.496→41.64 Å / SU ML: 0.34 / σ(F): 0.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2322 1253 5.09 %RANDOM
Rwork0.1947 ---
obs0.1967 24624 96.01 %-
all-25646 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.01 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso mean: 54.72 Å2
Baniso -1Baniso -2Baniso -3
1--3.5784 Å2-0 Å20 Å2
2---3.5784 Å2-0 Å2
3---7.1567 Å2
Refinement stepCycle: LAST / Resolution: 2.496→41.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3938 0 35 61 4034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014077
X-RAY DIFFRACTIONf_angle_d0.9615540
X-RAY DIFFRACTIONf_dihedral_angle_d13.9781557
X-RAY DIFFRACTIONf_chiral_restr0.079602
X-RAY DIFFRACTIONf_plane_restr0.006704
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4955-2.59540.33811260.2542232088
2.5954-2.71350.31321410.2429241491
2.7135-2.85650.27331300.2285250494
2.8565-3.03550.31731260.2227258896
3.0355-3.26970.29611380.2332260597
3.2697-3.59860.21091460.1938264498
3.5986-4.1190.20571500.1657268199
4.119-5.18790.17451450.14982733100
5.1879-41.64530.18511510.1784288299
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)
10.9810.1992-0.59431.28210.10720.4657-0.0931-0.1533-0.03860.42820.20840.01980.1124-0.102-0.09140.34180.09660.00920.33460.08080.226330.47987.911335.6924
21.2813-0.3029-0.29631.58530.50330.31580.01570.0372-0.0585-0.04440.0091-0.124-0.0433-0.0085-0.03590.13820.0051-0.02990.19530.00850.155341.61795.497112.1024
31.9099-0.1173-0.42250.03650.12720.81420.0801-0.16970.4786-0.0856-0.075-0.0866-0.11640.0905-0.03860.30290.0450.04920.24290.02310.388936.652731.804625.8766
40.7612-0.6497-0.85921.42580.61210.97740.04360.00450.06070.0198-0.12240.02060.0999-0.13310.05990.23450.0492-0.05340.25870.00470.196710.668130.96625.0121
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 541:633)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 634:810)
3X-RAY DIFFRACTION3(CHAIN B AND RESID 542:629)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 630:811)

+
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