[English] 日本語
Yorodumi
- PDB-3pyi: Structure of the N-terminal domain of C. elegans SAS-6 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3pyi
TitleStructure of the N-terminal domain of C. elegans SAS-6
ComponentsSpindle assembly abnormal protein 6
KeywordsSTRUCTURAL PROTEIN / beta-sandwich / dimer / alpha-beta protein / cytoplasmic / centriolar
Function / homology
Function and homology information


centriole assembly / centriole replication / centrosome duplication / centriole / protein localization / regulation of cell cycle / protein domain specific binding / centrosome / identical protein binding / cytoplasm
Similarity search - Function
: / Centriolar protein SAS, helical domain / Spindle assembly abnormal protein 6, N-terminal domain / Dna Repair Protein Xrcc4; Chain: A, domain 1 / Spindle assembly abnormal protein 6, N-terminal / SAS-6, N-terminal domain superfamily / Centriolar protein SAS N-terminal / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Spindle assembly abnormal protein 6
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.104 Å
AuthorsVakonakis, I. / Steinmetz, M.O.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: Structural basis of the 9-fold symmetry of centrioles.
Authors: Kitagawa, D. / Vakonakis, I. / Olieric, N. / Hilbert, M. / Keller, D. / Olieric, V. / Bortfeld, M. / Erat, M.C. / Fluckiger, I. / Gonczy, P. / Steinmetz, M.O.
History
DepositionDec 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
B: Spindle assembly abnormal protein 6
A: Spindle assembly abnormal protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8497
Polymers38,8762
Non-polymers9725
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-5 kcal/mol
Surface area17120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.273, 73.153, 79.596
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and not (resid 18:27 or resid 58:62 or...
211chain B and not (resid 18:27 or resid 58:62 or...

-
Components

#1: Protein Spindle assembly abnormal protein 6


Mass: 19438.242 Da / Num. of mol.: 2 / Fragment: N-terminal domain, UNP residues 1-168 / Mutation: S123E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: sas-6, Y45F10D.9 / Plasmid: modified pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O62479
#2: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.63 Å3/Da / Density % sol: 53.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 30% v/v PEG200, 5% w/v PEG3000, 0.1 M MES, seeding with crushed original crystals, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 22, 2010
RadiationMonochromator: Bartels Monochromator with dual channel cut crystals in (+--+) geometry
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.104→73.153 Å / Num. all: 24437 / Num. obs: 24368 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 31.25 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 17.7
Reflection shellResolution: 2.104→2.22 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 4 / Num. unique all: 3498 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIX(phenix.autosol)model building
PHENIX(phenix.refine: 1.6_289)refinement
XSCALEdata scaling
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.104→50.678 Å / SU ML: 0.29 / Isotropic thermal model: Isotropic with TLS restraints / σ(F): 1.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2574 2220 4.94 %Random
Rwork0.2101 ---
obs0.2124 23106 97.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.464 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 45.83 Å2
Baniso -1Baniso -2Baniso -3
1-14.0832 Å2-0 Å2-0 Å2
2---11.7579 Å2-0 Å2
3----2.3252 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 2.104→50.678 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2317 0 49 146 2512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072445
X-RAY DIFFRACTIONf_angle_d1.0233285
X-RAY DIFFRACTIONf_dihedral_angle_d16.866955
X-RAY DIFFRACTIONf_chiral_restr0.072380
X-RAY DIFFRACTIONf_plane_restr0.004410
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A925X-RAY DIFFRACTIONPOSITIONAL
12B925X-RAY DIFFRACTIONPOSITIONAL0.05
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.1039-2.17910.34512280.28494223446497
2.1791-2.26630.31512200.26294304453398
2.2663-2.36950.28292240.23794306455198
2.3695-2.49440.2712240.22284285451598
2.4944-2.65070.31722250.21024318454998
2.6507-2.85530.28042200.21594299453099
2.8553-3.14260.26552220.224292451998
3.1426-3.59720.28612230.20944294451998
3.5972-4.53170.19882160.17574216443397
4.5317-50.69280.2052180.18324224445196
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)
10.249-0.1020.24642.93240.7521.68260.0321-0.0191-0.0460.14990.034-0.07340.0768-0.0275-0.06180.1255-0.01110.02680.18230.00620.18921.0494-9.290416.1836
20.7640.0706-0.20482.2110.26861.46140.10110.08430.1344-0.35690.0514-0.2524-0.23580.1155-0.13250.291-0.00670.00790.18160.00230.240.4763-2.1058-15.7368
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

+
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