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- PDB-3p86: Crystal structure of CTR1 kinase domain mutant D676N in complex w... -

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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 / gibberellin biosynthetic process / negative regulation of ethylene-activated signaling pathway / sugar mediated signaling pathway / 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 / gibberellin biosynthetic process / negative regulation of ethylene-activated signaling pathway / sugar mediated signaling pathway / 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 / : / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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. ...Ethylene-responsive protein kinase Le-CTR1 / : / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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


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


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.52 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

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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

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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)

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