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- PDB-4agh: Structural features of ssDNA binding protein MoSub1 from Magnapor... -

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Basic information

Entry
Database: PDB / ID: 4agh
TitleStructural features of ssDNA binding protein MoSub1 from Magnaporthe oryzae
ComponentsMOSUB1, TRANSCRIPTION COFACTOR
KeywordsTRANSCRIPTION / SSDNA BINDING PROTEIN
Function / homology
Function and homology information


positive regulation of transcription initiation by RNA polymerase II / 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
Transcriptional coactivator p15 (PC4) C-terminal domain-containing protein
Similarity search - Component
Biological speciesMAGNAPORTHE ORYZAE (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.787 Å
AuthorsHuang, J. / Zhao, Y. / Huang, D. / liu, J. / Peng, Y.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structural Features of the Single-Stranded DNA-Binding Protein Mosub1 from Magnaporthe Oryzae.
Authors: Huang, J. / Zhao, Y. / Huang, D. / Liu, H. / Justin, N. / Zhao, W. / Liu, J. / Peng, Y.
History
DepositionJan 27, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references
Revision 1.2May 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: MOSUB1, TRANSCRIPTION COFACTOR


Theoretical massNumber of molelcules
Total (without water)16,9181
Polymers16,9181
Non-polymers00
Water1,964109
1
A: MOSUB1, TRANSCRIPTION COFACTOR

A: MOSUB1, TRANSCRIPTION COFACTOR


Theoretical massNumber of molelcules
Total (without water)33,8362
Polymers33,8362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area3210 Å2
ΔGint-25.1 kcal/mol
Surface area9470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.109, 60.109, 114.406
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein MOSUB1, TRANSCRIPTION COFACTOR


Mass: 16917.803 Da / Num. of mol.: 1 / Fragment: RESIDUES 5-162
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MAGNAPORTHE ORYZAE (rice blast fungus) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: G4NEJ8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 59.8 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9715
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9715 Å / Relative weight: 1
ReflectionResolution: 1.79→57.2 Å / Num. obs: 12162 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 17.6 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 16.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
xia2data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.787→47.381 Å / SU ML: 0.29 / σ(F): 1.34 / Phase error: 16.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2048 582 4.8 %
Rwork0.1757 --
obs0.177 12162 99.51 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.434 Å2 / ksol: 0.386 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.1732 Å20 Å20 Å2
2---0.1732 Å20 Å2
3---0.3465 Å2
Refinement stepCycle: LAST / Resolution: 1.787→47.381 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms632 0 0 109 741
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006644
X-RAY DIFFRACTIONf_angle_d1.056863
X-RAY DIFFRACTIONf_dihedral_angle_d13.017245
X-RAY DIFFRACTIONf_chiral_restr0.07188
X-RAY DIFFRACTIONf_plane_restr0.005114
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7866-1.96640.25171460.21842781X-RAY DIFFRACTION99
1.9664-2.25090.18441440.16492844X-RAY DIFFRACTION100
2.2509-2.83590.20581520.16592876X-RAY DIFFRACTION100
2.8359-47.3980.20221400.17623079X-RAY DIFFRACTION99
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)
15.8731-2.986-4.33564.2494.01034.4157-0.3808-0.3777-0.37050.45980.134-0.12550.80370.26230.2220.27430.020.02690.18860.03680.2613-2.095717.00989.6805
24.46780.9364-2.27835.4385-2.29064.5072-0.08390.3218-0.263-0.19690.12290.07290.2696-0.1225-0.06280.1041-0.01860.02130.1443-0.02670.1813-8.673419.9824.4886
34.33861.2806-3.12023.1871-3.81076.8876-0.390.06-0.3328-0.25960.01340.18920.48750.0210.05460.2121-0.03960.08550.19190.00670.2316-13.356412.976812.0573
42.77351.62681.02524.74374.59186.7908-0.01950.04270.2528-0.29520.1496-0.1779-0.47290.3456-0.14920.11730.01380.02140.11480.00310.1811-5.848136.55558.5319
53.2544-3.1824-2.00793.89070.96222.57850.20630.69110.4964-0.0787-0.2-1.20680.10071.01950.06410.27390.02580.00510.5301-0.05880.4228-1.132238.611421.3105
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 38:54)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 55:76)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 77:85)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 86:110)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 111:117)

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