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- PDB-2cjj: Crystal Structure of the MYB domain of the RAD transcription fact... -

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Basic information

Entry
Database: PDB / ID: 2cjj
TitleCrystal Structure of the MYB domain of the RAD transcription factor from Antirrhinum majus
ComponentsRADIALIS
KeywordsDNA BINDING PROTEIN / PLANT DEVELOPMENT / DNA-BINDING PROTEIN / MYB TRANSCRIPTION FACTOR / DNA-BINDING / NUCLEAR PROTEIN / FLORAL ASYMMETRY
Function / homology
Function and homology information


determination of dorsal/ventral asymmetry / flower development / DNA-binding transcription factor activity / nucleus
Similarity search - Function
Transcription factor RADIALIS-like / SANT domain profile. / SANT domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / Homeodomain-like / SANT/Myb domain / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcription factor RADIALIS
Similarity search - Component
Biological speciesANTIRRHINUM MAJUS (snapdragon)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 1.9 Å
AuthorsStevenson, C.E.M. / Burton, N. / Costa, M.M. / Nath, U. / Dixon, R.A. / Coen, E.S. / Lawson, D.M.
Citation
Journal: Proteins: Struct., Funct., Bioinf. / Year: 2006
Title: Crystal Structure of the Myb Domain of the Rad Transcription Factor from Antirrhinum Majus.
Authors: Stevenson, C.E.M. / Burton, N. / Costa, M.M. / Nath, U. / Dixon, R.A. / Coen, E.S. / Lawson, D.M.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Crystallisation and Preliminary X-Ray Analysis of the Rad Protein from Antirrhinum Majus
Authors: Stevenson, C.E.M. / Burton, N. / Costa, M. / Nath, U. / Dixon, R.A. / Coen, E.S. / Lawson, D.M.
History
DepositionApr 4, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 12, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RADIALIS


Theoretical massNumber of molelcules
Total (without water)10,7951
Polymers10,7951
Non-polymers00
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)44.594, 44.594, 71.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein RADIALIS


Mass: 10795.235 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 8 KDA PROTEOLYTIC FRAGMENT, MYB DOMAIN / Source: (gene. exp.) ANTIRRHINUM MAJUS (snapdragon) / Plasmid: PRSET A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q58FS3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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 %
Crystal growpH: 9.5 / Details: pH 9.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 18, 2004 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→37.9 Å / Num. obs: 6112 / % possible obs: 98.6 % / Observed criterion σ(I): 3 / Redundancy: 10.8 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 33.3
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 3.6 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXCDphasing
SHELXDphasing
SHELXEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.9→37.9 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.93 / SU B: 9.067 / SU ML: 0.125 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25 278 4.6 %RANDOM
Rwork0.215 ---
obs0.216 5727 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.04 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2---0.25 Å20 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms512 0 0 49 561
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.022525
X-RAY DIFFRACTIONr_bond_other_d0.0020.02374
X-RAY DIFFRACTIONr_angle_refined_deg1.9341.949710
X-RAY DIFFRACTIONr_angle_other_deg1.1073905
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.758562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.08723.84626
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.9391591
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.321154
X-RAY DIFFRACTIONr_chiral_restr0.1320.273
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02578
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02108
X-RAY DIFFRACTIONr_nbd_refined0.2170.2113
X-RAY DIFFRACTIONr_nbd_other0.1880.2351
X-RAY DIFFRACTIONr_nbtor_refined0.1950.2255
X-RAY DIFFRACTIONr_nbtor_other0.0880.2280
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2220.238
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1320.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2410.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.050.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9911.5346
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.382508
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3683243
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2134.5202
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.508 21
Rwork0.447 421
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)
19.73951.9563-3.36559.4114-2.363115.3950.1016-0.0617-0.09010.61950.06640.54150.5486-1.1493-0.168-0.0983-0.04140.0155-0.06350.0332-0.10342.86956.36312.2563
20.0605-0.46630.27858.56193.48377.66020.0499-0.17260.14170.24370.2043-0.8496-0.14180.629-0.2543-0.1167-0.0096-0.0367-0.1391-0.0077-0.05713.361415.33529.908
38.6975-9.7107-1.608523.83312.79022.0691-0.1142-0.36410.12530.85150.1712-0.0453-0.0394-0.0567-0.0570.0035-0.0166-0.0158-0.08840.0021-0.15299.52299.320417.7168
45.14022.29225.13447.3673-0.751612.7387-0.194-0.23660.32090.21860.1137-0.1666-0.54160.36410.0803-0.14970.02180.0064-0.1389-0.0162-0.111918.0851-5.892818.6528
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 20
2X-RAY DIFFRACTION2A21 - 41
3X-RAY DIFFRACTION3A42 - 57
4X-RAY DIFFRACTION4A58 - 70

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