[English] 日本語
Yorodumi
- PDB-3e8t: Crystal Structure of Epiphyas postvittana Takeout 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3e8t
TitleCrystal Structure of Epiphyas postvittana Takeout 1
ComponentsTakeout-like protein 1
KeywordsTRANSPORT PROTEIN / Takeout / Epiphyas postvittana
Function / homology
Function and homology information


extracellular space
Similarity search - Function
TULIP domain / Haemolymph juvenile hormone binding / Takeout superfamily / Haemolymph juvenile hormone binding protein (JHBP) / Juvenile hormone binding protein domains in insects. / Bactericidal permeability-increasing protein; domain 1 / Super Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquinone-8 / Takeout-like protein 1
Similarity search - Component
Biological speciesEpiphyas postvittana (butterflies/moths)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsHamiaux, C. / Stanley, D. / Greenwood, D.R. / Baker, E.N. / Newcomb, R.D.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Crystal structure of Epiphyas postvittana takeout 1 with bound ubiquinone supports a role as ligand carriers for takeout proteins in insects
Authors: Hamiaux, C. / Stanley, D. / Greenwood, D.R. / Baker, E.N. / Newcomb, R.D.
History
DepositionAug 20, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Takeout-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2392
Polymers24,5121
Non-polymers7271
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.454, 45.178, 53.778
Angle α, β, γ (deg.)90.000, 108.840, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Takeout-like protein 1 / Takeout 1


Mass: 24512.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Epiphyas postvittana (butterflies/moths)
Gene: takeout-like 1 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-Gami2 / References: UniProt: B5ABT1
#2: Chemical ChemComp-UQ8 / Ubiquinone-8 / 2,3-dimethoxy-5-methyl-6-[(6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-oc taen-1-yl]cyclohexa-2,5-diene-1,4-dione


Mass: 727.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C49H74O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.13 Å3/Da / Density % sol: 42.31 % / Mosaicity: 0.674 °
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: 50mM MES pH 6.2-6.7, 20-25% PEG 3000, pH 6.5, VAPOR DIFFUSION, temperature 291K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-00711.5418
SYNCHROTRONSSRL BL9-220.97951
Detector
TypeIDDetectorDate
MAR scanner 345 mm plate1IMAGE PLATEAug 7, 2007
MARMOSAIC 325 mm CCD2CCDDec 16, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1Si 111
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.979511
ReflectionRedundancy: 35.9 % / Av σ(I) over netI: 8.9 / Number: 962803 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / D res high: 1.61 Å / D res low: 24.19 Å / Num. obs: 26782 / % possible obs: 97.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
5.0624.2194.610.0430.04334.3
3.585.0699.610.0410.04136.4
2.923.5810010.0450.04537.3
2.532.9210010.050.0537.4
2.262.5310010.0520.05237
2.062.2610010.0610.06136.6
1.912.0610010.0750.07536.2
1.791.9110010.1060.10635.8
1.691.7999.910.1550.15535.3
1.61.698710.2310.23133.6
ReflectionResolution: 1.3→33.787 Å / Num. obs: 48865 / % possible obs: 96.1 % / Redundancy: 6.9 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.041 / Rsym value: 0.041
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 1.9 / Num. measured all: 26815 / Num. unique all: 5755 / Rsym value: 0.407 / % possible all: 78.3

-
Phasing

PhasingMethod: SAD
Phasing MAD set
IDR cullis acentricR cullis centricHighest resolution (Å)Lowest resolution (Å)Reflection acentricReflection centric
ISO_1001.6124.19254091360
ANO_10.90901.6124.19253390
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricReflection acentricReflection centric
ISO_16.92-24.190026356
ISO_14.99-6.920050269
ISO_14.11-4.990066369
ISO_13.57-4.110079470
ISO_13.2-3.570088669
ISO_12.92-3.200100768
ISO_12.71-2.9200109569
ISO_12.54-2.7100115267
ISO_12.39-2.5400124472
ISO_12.27-2.3900131571
ISO_12.17-2.2700139567
ISO_12.08-2.1700143570
ISO_11.99-2.0800151771
ISO_11.92-1.9900158371
ISO_11.86-1.9200163473
ISO_11.8-1.8600166466
ISO_11.75-1.800175671
ISO_11.7-1.7500180666
ISO_11.65-1.700184765
ISO_11.61-1.6500185160
ANO_16.92-24.190.68702470
ANO_14.99-6.920.6305020
ANO_14.11-4.990.80506570
ANO_13.57-4.110.77507930
ANO_13.2-3.570.74808850
ANO_12.92-3.20.746010070
ANO_12.71-2.920.757010950
ANO_12.54-2.710.778011520
ANO_12.39-2.540.816012440
ANO_12.27-2.390.863013150
ANO_12.17-2.270.874013950
ANO_12.08-2.170.891014350
ANO_11.99-2.080.912015170
ANO_11.92-1.990.933015830
ANO_11.86-1.920.949016340
ANO_11.8-1.860.971016640
ANO_11.75-1.80.974017560
ANO_11.7-1.750.982018060
ANO_11.65-1.70.988018470
ANO_11.61-1.650.988018050
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
1-12.215-16.144-23.809S20.061.43
2-12.188-9.761-33.723S20.221.27
3-0.32-13.35-15.694S19.361.02
43.071-15.222-14.682S26.241.2
5-2.3-13.526-16.006S18.461.02
6-31.993-6.218-3.041S15.230.79
7-32.793-16.511-20.515S37.361.2

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.33data scaling
SHARPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.3→31.16 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.961 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.922 / SU B: 1.374 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.182 2472 5.1 %RANDOM
Rwork0.142 ---
obs0.144 48848 96.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.77 Å2 / Biso mean: 20.639 Å2 / Biso min: 8.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å2-0.04 Å2
2---0.01 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.3→31.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1784 0 53 308 2145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221886
X-RAY DIFFRACTIONr_bond_other_d0.0010.021280
X-RAY DIFFRACTIONr_angle_refined_deg1.6651.9882563
X-RAY DIFFRACTIONr_angle_other_deg0.9153.0063124
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2875246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.66526.58582
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.75515358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.172151
X-RAY DIFFRACTIONr_chiral_restr0.1070.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022075
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02337
X-RAY DIFFRACTIONr_nbd_refined0.2380.2366
X-RAY DIFFRACTIONr_nbd_other0.1830.21280
X-RAY DIFFRACTIONr_nbtor_refined0.1850.2915
X-RAY DIFFRACTIONr_nbtor_other0.0910.21037
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2320.2202
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2410.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2190.247
X-RAY DIFFRACTIONr_mcbond_it2.76821454
X-RAY DIFFRACTIONr_mcbond_other1.2232459
X-RAY DIFFRACTIONr_mcangle_it3.22631826
X-RAY DIFFRACTIONr_scbond_it4.2983888
X-RAY DIFFRACTIONr_scangle_it5.2384.5722
X-RAY DIFFRACTIONr_rigid_bond_restr2.65233840
X-RAY DIFFRACTIONr_sphericity_free8.4353308
X-RAY DIFFRACTIONr_sphericity_bonded4.43633117
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 125 -
Rwork0.21 2537 -
all-2662 -
obs--71.52 %

+
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