[English] 日本語
Yorodumi
- PDB-5zg9: Crystal structure of MoSub1-ssDNA complex in phosphate buffer -

+
Open data


ID or keywords:

Loading...

-
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


regulation of DNA-templated transcription / DNA binding / nucleus
Similarity search - Function
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) / PC4 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Phosphate


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more