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- PDB-6jui: The atypical Myb-like protein Cdc5 contains two distinct nucleic ... -

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Basic information

Entry
Database: PDB / ID: 6jui
TitleThe atypical Myb-like protein Cdc5 contains two distinct nucleic acid-binding surfaces
ComponentsPre-mRNA-splicing factor CEF1
KeywordsDNA BINDING PROTEIN / crystal / DNA binding domain / Myb domain / rice blast fungus / RNA binding
Function / homology
Function and homology information


nucleolar peripheral inclusion body / post-mRNA release spliceosomal complex / mRNA cis splicing, via spliceosome / Prp19 complex / DNA binding / cytosol
Similarity search - Function
Pre-mRNA splicing factor component Cdc5p/Cef1, C-terminal / : / : / pre-mRNA splicing factor component / Myb-like DNA-binding domain / Myb-type HTH DNA-binding domain profile. / Myb domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
Pre-mRNA-splicing factor CEF1
Similarity search - Component
Biological speciesMagnaporthe oryzae (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.402 Å
AuthorsWang, C. / Li, G. / Li, M. / Yang, J. / Liu, J.
CitationJournal: Biochem.J. / Year: 2019
Title: Two distinct nucleic acid binding surfaces of Cdc5 regulate development.
Authors: Wang, C. / Li, M. / Li, G. / Liu, X. / Zhao, W. / Yu, B. / Liu, J. / Yang, J. / Peng, Y.L.
History
DepositionApr 14, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pre-mRNA-splicing factor CEF1


Theoretical massNumber of molelcules
Total (without water)13,5081
Polymers13,5081
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7210 Å2
Unit cell
Length a, b, c (Å)72.780, 76.277, 54.409
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Pre-mRNA-splicing factor CEF1 / MoCdc5 DNA Binding Domain


Mass: 13507.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnaporthe oryzae (rice blast fungus) / Gene: CEF1, MGG_01426 / Production host: Escherichia coli (E. coli) / References: UniProt: Q52G60
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 40% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.402→38.14 Å / Num. obs: 11354 / % possible obs: 99.29 % / Redundancy: 7.4 % / Net I/σ(I): 22.1
Reflection shellResolution: 2.402→2.488 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.402→38.139 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.31 / Phase error: 34.12
RfactorNum. reflection% reflection
Rfree0.2705 1097 9.66 %
Rwork0.2342 --
obs0.2378 11354 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.402→38.139 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms836 0 0 2 838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007854
X-RAY DIFFRACTIONf_angle_d0.8831156
X-RAY DIFFRACTIONf_dihedral_angle_d8.708522
X-RAY DIFFRACTIONf_chiral_restr0.048126
X-RAY DIFFRACTIONf_plane_restr0.005144
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.402-2.51130.38561370.23421280X-RAY DIFFRACTION98
2.5113-2.64370.24641370.33121263X-RAY DIFFRACTION99
2.6437-2.80930.38621430.2771298X-RAY DIFFRACTION100
2.8093-3.02610.33611320.28051300X-RAY DIFFRACTION100
3.0261-3.33050.34441480.25941256X-RAY DIFFRACTION100
3.3305-3.8120.28151300.22921293X-RAY DIFFRACTION100
3.812-4.80130.19581350.20481303X-RAY DIFFRACTION100
4.8013-38.1390.26621350.20741264X-RAY DIFFRACTION98
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)
17.7059-1.53794.40517.7574-2.22734.32770.1411-0.6384-0.52360.2670.47720.4726-0.78740.2726-0.9050.4514-0.01940.01010.8355-0.13380.6081-8.5699-20.61314.7077
26.67991.5964-0.95556.99350.56272.72750.07490.5256-1.0555-0.2258-0.28980.29650.84130.2602-0.34550.65290.0168-0.11330.7459-0.0740.7983-4.2931-27.08622.5886
36.93233.8316-3.65996.175-2.00312.6420.6778-0.06271.06091.0641-0.25860.4567-0.9739-0.3018-0.22790.6799-0.0626-0.00470.7117-0.10510.75113.4701-10.6123-1.4828
47.7522-3.74211.61722.56490.85643.07090.74070.56091.9254-1.3536-0.6136-1.0581-1.20381.1307-0.09810.6451-0.2189-0.050.82480.0740.687117.126-8.9799-11.8132
55.0832-1.36130.14611.9765-2.55163.64540.1499-2.089-1.31160.5507-0.4553-0.48450.43081.48640.21110.6964-0.0235-0.14251.50190.08380.77715.5543-18.3865-7.8769
64.78220.47692.05254.00560.12869.58010.1509-0.1545-0.0980.44760.17120.5678-0.6716-0.3917-0.21010.4819-0.0684-0.00850.578-0.07320.52597.9634-12.7696-17.5335
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 50 )
3X-RAY DIFFRACTION3chain 'A' and (resid 51 through 62 )
4X-RAY DIFFRACTION4chain 'A' and (resid 63 through 75 )
5X-RAY DIFFRACTION5chain 'A' and (resid 76 through 90 )
6X-RAY DIFFRACTION6chain 'A' and (resid 91 through 108 )

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