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- PDB-5zg9: Crystal structure of MoSub1-ssDNA complex in phosphate buffer -

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Basic information

Entry
Database: PDB / ID: 5zg9
TitleCrystal structure of MoSub1-ssDNA complex in phosphate buffer
Components
  • DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*G)-3')
  • MoSub1
KeywordsDNA BINDING PROTEIN/DNA / ssDNA binding protein / transcriptional co-factor / PC4-like protein / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


positive regulation of transcription initiation by RNA polymerase II / transcription regulator complex / transcription coactivator activity / DNA binding / nucleus
Similarity search - Function
RNA polymerase II transcriptional coactivator Sub1/Tcp4-like / Transcriptional coactivator p15 (PC4), C-terminal / Transcriptional Coactivator p15 (PC4) / Transcriptional Coactivator Pc4; Chain A / ssDNA-binding transcriptional regulator / Transcriptional Co-activator pc4; Chain A / Roll / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / DNA / DNA (> 10) / Transcriptional coactivator p15 (PC4) C-terminal domain-containing protein
Similarity search - Component
Biological speciesMagnaporthe oryzae (rice blast fungus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsZhao, Y. / Huang, J. / Liu, H. / Yi, L. / Wang, S. / Zhang, X. / Liu, J.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2017YFD0200500 China
Ministry of Science and Technology (China)2017YFD0201100 China
CitationJournal: Proteins / Year: 2019
Title: The effect of phosphate ion on the ssDNA binding mode of MoSub1, a Sub1/PC4 homolog from rice blast fungus.
Authors: Zhao, Y. / Zhang, Y. / Huang, J. / Wang, S. / Yi, L. / Zhang, X. / Xu, M. / Fang, X. / Liu, J.
History
DepositionMar 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2019Provider: 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: MoSub1
B: MoSub1
C: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8505
Polymers42,6613
Non-polymers1902
Water2,414134
1
A: MoSub1
B: MoSub1
C: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*G)-3')
hetero molecules

A: MoSub1
B: MoSub1
C: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,70110
Polymers85,3216
Non-polymers3804
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_758-x+2,y,-z+31
Buried area13640 Å2
ΔGint-118 kcal/mol
Surface area20350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.010, 80.190, 76.910
Angle α, β, γ (deg.)90.00, 91.88, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11B-245-

HOH

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Components

#1: Protein MoSub1


Mass: 18298.322 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnaporthe oryzae (strain P131) (fungus)
Strain: P131 / Gene: OOW_P131scaffold01307g15 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: L7IX95
#2: DNA chain DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*G)-3')


Mass: 6063.912 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe authors performed crystallization using the full-length MoSub1 with His-tag, but they doubted ...The authors performed crystallization using the full-length MoSub1 with His-tag, but they doubted that it was digested by protease during the purification process. Thus, they don't know the exact protein length in the crystals.

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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

Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.8 M K2HPO4-NaH2PO4 pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.04→40.095 Å / Num. obs: 15521 / % possible obs: 95.26 % / Redundancy: 3.7 % / Net I/σ(I): 22.11
Reflection shellResolution: 2.04→2.113 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→40.095 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 2.04 / Phase error: 26.67
RfactorNum. reflection% reflection
Rfree0.2244 1495 5.1 %
Rwork0.1764 --
obs0.1788 15521 91.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.04→40.095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1284 240 10 134 1668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071585
X-RAY DIFFRACTIONf_angle_d1.2642181
X-RAY DIFFRACTIONf_dihedral_angle_d19.933616
X-RAY DIFFRACTIONf_chiral_restr0.086227
X-RAY DIFFRACTIONf_plane_restr0.004247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0401-2.1060.32571390.24522478X-RAY DIFFRACTION89
2.106-2.18120.36531330.22872483X-RAY DIFFRACTION91
2.1812-2.26860.29081270.22272583X-RAY DIFFRACTION93
2.2686-2.37180.3161100.22112585X-RAY DIFFRACTION93
2.3718-2.49680.31781280.24192440X-RAY DIFFRACTION89
2.4968-2.65320.31791400.24132561X-RAY DIFFRACTION93
2.6532-2.8580.31381610.22682535X-RAY DIFFRACTION93
2.858-3.14550.21851640.20352525X-RAY DIFFRACTION93
3.1455-3.60050.21921530.15382456X-RAY DIFFRACTION90
3.6005-4.53520.14641250.12572647X-RAY DIFFRACTION95
4.5352-40.10270.16891150.15292532X-RAY DIFFRACTION91
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)
18.39583.3264-2.53966.8938-1.68015.8054-0.0535-0.27350.1735-0.738-0.27020.1121-0.8412-0.13270.37330.41270.0246-0.09020.24610.010.273848.939724.465596.3001
24.1261-0.7310.15413.17480.86094.5617-0.02290.1230.061-0.1114-0.0558-0.379-0.31860.28720.03570.2698-0.02370.03040.24960.04920.258655.297717.7942102.6572
35.5465-4.4895-3.4168.55754.71827.18820.1721-0.21960.2848-0.2687-0.1857-0.3486-0.68260.0866-0.04240.21130.0045-0.04090.2980.01710.249951.663719.3181107.8917
49.38423.1145-0.30245.13770.10984.5261-0.08040.6826-0.0398-0.84480.13740.55630.325-0.2267-0.05080.4357-0.0014-0.07590.2439-0.00680.266845.00432.553692.9511
54.19862.22742.16786.20151.01233.2406-0.1105-0.0941-0.29250.2530.2025-0.28740.46270.2096-0.00950.49830.0720.04660.2439-0.03790.41549.722-6.077599.7954
63.09830.32730.69864.6991-0.28324.47910.08250.0022-0.087-0.2858-0.04290.24010.2561-0.1251-0.0150.25040.0215-0.03280.1434-0.0390.205548.40076.3125100.7439
72.34430.8316-1.18031.7268-1.25580.98830.1180.05120.0693-0.09930.00740.14630.0790.0484-0.09850.2839-0.01030.0190.39350.02110.385843.068311.9016115.2368
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 34 through 54 )
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 75 )
3X-RAY DIFFRACTION3chain 'A' and (resid 76 through 90 )
4X-RAY DIFFRACTION4chain 'A' and (resid 91 through 116 )
5X-RAY DIFFRACTION5chain 'B' and (resid 34 through 54 )
6X-RAY DIFFRACTION6chain 'B' and (resid 55 through 115 )
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 12 )

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