[English] 日本語
Yorodumi
- PDB-2xfv: Structure of the amino-terminal domain from the cell-cycle regula... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xfv
TitleStructure of the amino-terminal domain from the cell-cycle regulator Swi6
ComponentsREGULATORY PROTEIN SWI6
KeywordsCELL CYCLE / CELL-CYCLE / REGULATION
Function / homology
Function and homology information


SBF transcription complex / MBF transcription complex / positive regulation of reciprocal meiotic recombination / G1/S transition of mitotic cell cycle / cellular response to heat / transcription coactivator activity / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytoplasm
Similarity search - Function
Mlu1-box Binding Protein; DNA-binding Domain - #30 / Swi6, N-terminal / Swi6 N-terminal domain / : / Mlu1-box Binding Protein; DNA-binding Domain / Ankyrin repeat / Ankyrin repeat region circular profile. / Ankyrin repeat profile. / ankyrin repeats / Ankyrin repeat ...Mlu1-box Binding Protein; DNA-binding Domain - #30 / Swi6, N-terminal / Swi6 N-terminal domain / : / Mlu1-box Binding Protein; DNA-binding Domain / Ankyrin repeat / Ankyrin repeat region circular profile. / Ankyrin repeat profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / CACODYLATE ION / Regulatory protein SWI6
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsSmerdon, S.J. / Goldstone, D.C. / Taylor, I.A.
CitationJournal: Proteins / Year: 2010
Title: Structure of the Amino-Terminal Domain from the Cell-Cycle Regulator Swi6S
Authors: Taylor, I.A. / Goldstone, D.C. / Pala, P. / Haire, L. / Smerdon, S.J.
History
DepositionMay 27, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1May 19, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: REGULATORY PROTEIN SWI6
B: REGULATORY PROTEIN SWI6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,63210
Polymers29,0402
Non-polymers5938
Water5,927329
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-42.4 kcal/mol
Surface area11930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.934, 69.934, 297.944
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-1113-

ACT

21A-1113-

ACT

31A-1114-

CAC

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein REGULATORY PROTEIN SWI6 / CELL-CYCLE BOX FACTOR SUBUNIT SWI6 / TRANS-ACTING ACTIVATOR OF HO ENDONUCLEASE GENE / MBF SUBUNIT P90


Mass: 14519.916 Da / Num. of mol.: 2 / Fragment: AMINO-TERMINAL DOMAIN, RESIDUES 2-126
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P09959

-
Non-polymers , 5 types, 337 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.38 Å3/Da / Density % sol: 63.6 % / Description: NONE
Crystal growpH: 6.5
Details: 5-15MG/ML PROTEIN, 10% PEG4000, 0.1M NA-CACODYLATE, 20MM CA-ACETATE, 0.2M NH4CL, PH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: May 1, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 35176 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 10.6 % / Biso Wilson estimate: 24.04 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 37
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 6.8 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.9→19.784 Å / SU ML: 0.2 / σ(F): 0.09 / Phase error: 16.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1962 1691 5 %
Rwork0.1705 --
obs0.1717 34034 96.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.056 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso mean: 30.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.7356 Å20 Å20 Å2
2--0.7356 Å20 Å2
3----1.4713 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.784 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1774 0 30 329 2133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081914
X-RAY DIFFRACTIONf_angle_d1.012614
X-RAY DIFFRACTIONf_dihedral_angle_d17.647722
X-RAY DIFFRACTIONf_chiral_restr0.077283
X-RAY DIFFRACTIONf_plane_restr0.005352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.95590.23571170.19052473X-RAY DIFFRACTION90
1.9559-2.0190.18041240.16752546X-RAY DIFFRACTION94
2.019-2.09110.18981490.16082569X-RAY DIFFRACTION95
2.0911-2.17470.18121340.15342659X-RAY DIFFRACTION97
2.1747-2.27350.22471350.15642651X-RAY DIFFRACTION97
2.2735-2.39320.22111370.16662645X-RAY DIFFRACTION96
2.3932-2.54290.18741530.15992686X-RAY DIFFRACTION98
2.5429-2.73870.19421480.17322697X-RAY DIFFRACTION97
2.7387-3.01350.21651560.16682746X-RAY DIFFRACTION98
3.0135-3.44760.19521600.17112773X-RAY DIFFRACTION99
3.4476-4.3360.16691310.1522882X-RAY DIFFRACTION99
4.336-19.78470.18161470.17683016X-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)
11.22150.0755-0.28423.8177-0.51772.47320.2609-0.16920.20420.4143-0.18760.6121-0.2677-0.53080.06170.11880.02790.02560.2733-0.05410.2152-17.330938.360116.1844
20.44020.0930.1430.4682-0.37730.45410.2521-0.2272-0.23680.1552-0.34180.56840.2235-0.15120.02730.0927-0.03930.04140.3415-0.0420.3128-27.763425.064616.2196
31.084-0.26510.22550.13580.27941.499-0.0113-0.1292-0.1005-0.0233-0.08210.0881-0.1631-0.01930.07330.1137-0.0222-0.00020.222-0.04640.1263-10.569433.54715.5638
40.72370.08350.41270.95540.40221.7038-0.0223-0.0385-1.0137-0.0627-0.10540.24070.2318-0.60950.15980.1249-0.09360.01560.2445-0.08160.3634-17.790316.660710.9093
50.5287-0.13590.65610.0465-0.19690.9384-0.5285-0.8914-0.88860.4305-0.20990.10650.4557-0.40570.67030.2314-0.01690.08360.50670.01970.3615-22.084117.973319.6269
60.39520.12020.16670.7092-0.05150.08710.0548-0.1788-0.46370.2924-0.09660.39030.02140.04630.05490.1937-0.05090.04830.2746-0.00560.3362-6.873817.295720.281
71.5304-0.3267-0.7090.40350.1240.65030.0028-0.0222-0.2067-0.07410.08830.0302-0.11370.1474-0.05810.0894-0.02080.01560.1614-0.04960.1146-2.781126.070614.9541
80.70270.15850.32430.30980.10822.48480.07920.335-0.0148-0.07170.0636-0.0066-0.35470.5322-0.12760.0766-0.02930.01930.181-0.01760.0818-5.480131.956813.0387
90.27470.1439-0.01830.0771-0.01990.00720.05340.2908-0.0387-0.0645-0.07630.0382-0.00650.03060.01050.1333-0.0099-0.01310.2829-0.0620.1422-15.203826.98564.6217
102.3556-1.23392.6329.4327-1.74082.9876-0.05240.46980.0427-0.52680.39811.282-0.3847-0.4161-0.25450.20660.033-0.03480.3823-0.02930.2722-21.803835.32685.8275
115.69450.74470.06570.72911.5794.1001-0.41020.06841.142-0.60550.17160.2488-0.88960.00870.27660.4352-0.03-0.07310.27480.01110.3758-13.429944.0451-0.1269
120.552-0.02790.4580.7143-0.32980.50110.14440.07060.4596-0.002-0.1096-0.3028-0.220.3828-0.0290.1607-0.0338-0.00640.3736-0.09240.3936-11.418740.5606-10.7926
131.161-0.8215-0.11430.6532-0.01910.1596-0.10950.11730.6585-0.08070.10590.0502-0.30150.15970.0720.10110.0502-0.00620.5059-0.08480.3507-4.086235.1776-18.5262
141.3220.2146-0.07530.10380.22030.45-0.1242-0.2430.73450.07340.07410.0581-0.0047-0.01880.11620.09070.0352-0.02770.2572-0.14940.2591-22.937441.6312-7.5676
150.184-0.37770.22720.8251-0.46780.46660.18920.57480.0014-0.0187-0.36710.05330.06970.27320.16220.0969-0.00370.01030.39-0.07520.2045-18.648734.2595-17.87
164.56-2.16963.40732.4573-1.21972.7272-0.14911.29620.0782-0.4762-0.0782-0.66210.16560.3781-0.32940.12010.04690.0250.5144-0.15120.2549-13.689728.3058-22.5544
174.03470.37760.92930.5181-0.7881.7928-0.05460.60570.217-0.2689-0.0990.02840.2777-0.29880.09930.07580.02670.02640.4272-0.00810.1306-26.300132.2349-27.5476
180.4465-0.00490.31430.12650.07780.25520.01360.3711-0.2810.00830.10480.01910.09390.2013-0.10170.08460.0348-0.0240.2561-0.07940.1433-27.740627.7685-18.3244
194.0963-0.8756-1.08963.1818-1.61531.87280.34910.31640.98860.0908-0.16930.1284-0.3494-0.1014-0.08770.20760.0289-0.00990.2121-0.0130.3579-32.909444.4899-14.0021
200.3592-0.36260.64250.4422-0.37751.82640.0633-0.39350.1806-0.04150.43870.05620.0086-0.4787-0.28830.12230.0332-0.0050.2831-0.0410.1993-27.547538.2955-11.3664
211.0178-0.05830.20370.24940.19530.86050.39280.3042-0.2293-0.0204-0.1889-0.11280.12590.1306-0.16870.13180.0187-0.03170.2932-0.08390.1601-16.366729.3873-6.6154
222.49910.19821.35062.55711.80441.9539-0.6814-0.18510.8131-0.13430.65050.2193-0.45480.70940.0490.23790.0259-0.04210.3321-0.10040.2981-13.994541.13865.6785
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 2:8)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 9:17)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 18:36)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 37:48)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 49:54)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 55:63)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 64:78)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 79:86)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 87:96)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 97:103)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 104:109)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 2:12)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 13:17)
14X-RAY DIFFRACTION14(CHAIN B AND RESID 18:31)
15X-RAY DIFFRACTION15(CHAIN B AND RESID 32:38)
16X-RAY DIFFRACTION16(CHAIN B AND RESID 39:55)
17X-RAY DIFFRACTION17(CHAIN B AND RESID 56:60)
18X-RAY DIFFRACTION18(CHAIN B AND RESID 61:72)
19X-RAY DIFFRACTION19(CHAIN B AND RESID 73:77)
20X-RAY DIFFRACTION20(CHAIN B AND RESID 78:84)
21X-RAY DIFFRACTION21(CHAIN B AND RESID 85:101)
22X-RAY DIFFRACTION22(CHAIN B AND RESID 102:109)

+
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