[English] 日本語
Yorodumi
- PDB-3ont: The Crystal Structure of Spot14, a modulator of lipogenesis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ont
TitleThe Crystal Structure of Spot14, a modulator of lipogenesis
ComponentsSpot 14 protein
KeywordsUNKNOWN FUNCTION / alpha-helical / helical bundle
Function / homology
Function and homology information


Carnitine shuttle / regulation of triglyceride biosynthetic process / regulation of lipid biosynthetic process / molecular function inhibitor activity / response to bacterium / lipid metabolic process / protein homodimerization activity / protein-containing complex / nucleoplasm / identical protein binding / cytosol
Similarity search - Function
Helix Hairpins - #1610 / Spot 14 family / : / Thyroid hormone-inducible hepatic protein Spot 14 / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
Thyroid hormone-inducible hepatic protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å
AuthorsColbert, C.L. / Kwon, H.J. / Deisenhofer, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Crystal structure of Spot 14, a modulator of fatty acid synthesis.
Authors: Colbert, C.L. / Kim, C.W. / Moon, Y.A. / Henry, L. / Palnitkar, M. / McKean, W.B. / Fitzgerald, K. / Deisenhofer, J. / Horton, J.D. / Kwon, H.J.
History
DepositionAug 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Spot 14 protein


Theoretical massNumber of molelcules
Total (without water)17,5391
Polymers17,5391
Non-polymers00
Water1086
1
A: Spot 14 protein

A: Spot 14 protein


Theoretical massNumber of molelcules
Total (without water)35,0782
Polymers35,0782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation43_555-x+1/2,-z+1/2,-y+1/21
Buried area5290 Å2
ΔGint-59 kcal/mol
Surface area12580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.951, 144.951, 144.951
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432

-
Components

#1: Protein Spot 14 protein / Thyroid hormone-inducible hepatic protein / SPOT14 / S14


Mass: 17538.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: S14, spot14, Thrsp / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q62264
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.62 Å3/Da / Density % sol: 66 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.100 M MES pH 6.0, 0.015 M magnesium chloride, 5% (w/v) polyethylene glycol 3000 and 30% (v/v) polyethylene glycol 200, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 26, 2009
RadiationMonochromator: sagittally focused Si 111 + sagittally focused Si 220
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.64→50 Å / Num. all: 7941 / Num. obs: 7919 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Biso Wilson estimate: 92.2 Å2 / Rsym value: 0.063 / Net I/σ(I): 14.9
Reflection shellResolution: 2.64→2.69 Å / Redundancy: 7.5 % / Num. unique all: 379 / Rsym value: 0.552 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000phasing
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.65→38.74 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.915 / SU B: 18.171 / SU ML: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24912 363 4.6 %RANDOM
Rwork0.22305 ---
all0.22424 7894 --
obs0.22424 7512 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.221 Å2
Refinement stepCycle: LAST / Resolution: 2.65→38.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms902 0 0 6 908
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022918
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.9711241
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.735109
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.43623.95343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.52215166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.24156
X-RAY DIFFRACTIONr_chiral_restr0.1140.2145
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021675
X-RAY DIFFRACTIONr_mcbond_it1.462558
X-RAY DIFFRACTIONr_mcangle_it2.7013908
X-RAY DIFFRACTIONr_scbond_it1.8373360
X-RAY DIFFRACTIONr_scangle_it2.5873333
LS refinement shellResolution: 2.648→2.717 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 36 -
Rwork0.33 528 -
obs--99.65 %
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)
19.0733-0.34552.61421.39860.28720.9037-0.160.07030.0871-0.09650.11940.3711-0.04680.11620.04070.2213-0.0223-0.04180.33460.08320.356550.806718.787768.7064
211.28832.0084.96320.40630.74332.59210.24850.216-0.3779-0.03030.0277-0.0070.30690.211-0.27610.2405-0.0129-0.03660.37090.07050.341453.72919.775368.6068
312.3312.85728.20351.02871.7945.6180.29590.6148-0.25880.0721-0.0912-0.09880.36880.4459-0.20470.222-0.01670.00060.37860.08580.332331.61410.988360.8276
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 45
2X-RAY DIFFRACTION2A49 - 76
3X-RAY DIFFRACTION3A105 - 149

+
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