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- PDB-3e8w: Crystal Structure of Epiphyas postvittana Takeout 1 -

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Basic information

Entry
Database: PDB / ID: 3e8w
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 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: Advisory / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Takeout-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2392
Polymers24,5121
Non-polymers7271
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.043, 54.051, 83.577
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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.: 83 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.73 % / Mosaicity: 1.32 °
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 30, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 11.3 % / Av σ(I) over netI: 6.3 / Number: 84738 / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / D res high: 2.5 Å / D res low: 45.408 Å / Num. obs: 7491 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
7.9134.619910.050.059.5
5.597.9110010.0630.06310.8
4.565.5910010.0580.05811.2
3.954.5610010.0610.06111.4
3.543.9510010.0790.07911.4
3.233.5410010.1120.11211.5
2.993.2310010.1690.16911.5
2.82.9999.910.2310.23111.5
2.642.899.910.2950.29511.4
2.52.6499.810.3890.38911.4
ReflectionResolution: 2.5→34.6 Å / Num. obs: 7491 / % possible obs: 99.9 % / Redundancy: 11.3 % / Biso Wilson estimate: 39.7 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.5-2.6411.40.38921201910550.38999.8
2.64-2.811.40.2952.61162210210.29599.9
2.8-2.9911.50.2313.3109579510.23199.9
2.99-3.2311.50.1694.5101758870.169100
3.23-3.5411.50.1126.695148270.112100
3.54-3.9511.40.079985597480.079100
3.95-4.5611.40.0611177436820.061100
4.56-5.5911.20.05811.564595770.058100
5.59-7.9110.80.06310.450194630.063100
7.91-34.619.50.059.626712800.0599

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å34.6 Å
Translation2.5 Å34.6 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.33data scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3E8T

3e8t


Resolution: 2.5→33.06 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.885 / Occupancy max: 1 / Occupancy min: 1 / SU B: 20.328 / SU ML: 0.24 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.338 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26 344 4.6 %RANDOM
Rwork0.183 ---
obs0.187 7458 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.33 Å2 / Biso mean: 19.626 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.19 Å20 Å20 Å2
2---0.36 Å20 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 2.5→33.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1719 0 53 83 1855
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221806
X-RAY DIFFRACTIONr_bond_other_d0.0010.021218
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.9872432
X-RAY DIFFRACTIONr_angle_other_deg0.8393.0062944
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7485218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.94226.31676
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.40115327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.907151
X-RAY DIFFRACTIONr_chiral_restr0.0740.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021954
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02322
X-RAY DIFFRACTIONr_nbd_refined0.2080.2362
X-RAY DIFFRACTIONr_nbd_other0.1740.21222
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2852
X-RAY DIFFRACTIONr_nbtor_other0.0870.2928
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.280
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1320.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1610.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.216
X-RAY DIFFRACTIONr_mcbond_it0.8331.51399
X-RAY DIFFRACTIONr_mcbond_other0.1081.5446
X-RAY DIFFRACTIONr_mcangle_it0.93621749
X-RAY DIFFRACTIONr_scbond_it1.6193850
X-RAY DIFFRACTIONr_scangle_it2.3784.5683
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 21 -
Rwork0.212 512 -
all-533 -
obs--99.63 %
Refinement TLS params.Method: refined / Origin x: 7.9133 Å / Origin y: 7.1268 Å / Origin z: 8.3861 Å
111213212223313233
T0.0301 Å20.0012 Å2-0.0021 Å2-0.0765 Å20.0093 Å2--0.0296 Å2
L0.145 °20.0008 °2-0.0781 °2-1.0763 °20.4562 °2--0.5582 °2
S-0.0267 Å °-0.0186 Å °-0.0219 Å °0.0131 Å °0.0178 Å °0.0671 Å °-0.0534 Å °0.0278 Å °0.0089 Å °

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