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- PDB-4g0s: Crystal Structure of Epiphyas postvittana Takeout 1 expressed in ... -

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Basic information

Entry
Database: PDB / ID: 4g0s
TitleCrystal Structure of Epiphyas postvittana Takeout 1 expressed in Sf9 cells
ComponentsTakeout-like protein 1
KeywordsTRANSPORT PROTEIN
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
MYRISTIC ACID / Takeout-like protein 1
Similarity search - Component
Biological speciesEpiphyas postvittana (butterflies/moths)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.191 Å
AuthorsHamiaux, C. / Baker, E.N. / Newcomb, R.D.
Citation
Journal: J.Struct.Biol. / Year: 2013
Title: Ligand promiscuity within the internal cavity of Epiphyas postvittana Takeout 1 protein.
Authors: Hamiaux, C. / Basten, L. / Greenwood, D.R. / Baker, E.N. / Newcomb, R.D.
#1: Journal: 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
DepositionJul 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Takeout-like protein 1
B: Takeout-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9386
Polymers49,0252
Non-polymers9134
Water1,856103
1
A: Takeout-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9693
Polymers24,5121
Non-polymers4572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Takeout-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9693
Polymers24,5121
Non-polymers4572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.835, 55.184, 87.279
Angle α, β, γ (deg.)90.000, 90.220, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 4 / Auth seq-ID: 2 - 220 / Label seq-ID: 2 - 220

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Takeout-like protein 1


Mass: 24512.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Epiphyas postvittana (butterflies/moths)
Gene: takeout 1 / Plasmid: pDEST8 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: B5ABT1
#2: Chemical
ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H28O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

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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: 2.25 Å3/Da / Density % sol: 45.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6
Details: 0.1M MES, 26-31% PEG 3000, pH 6.0, vapor diffusion, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95468 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95468 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.546
11h,-k,-l20.454
ReflectionResolution: 2.191→45.835 Å / Num. all: 22359 / Num. obs: 22359 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.13 / Rsym value: 0.13 / Net I/σ(I): 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.191-2.323.60.34921162632330.349100
2.32-2.463.60.2852.61104730700.285100
2.46-2.633.60.2213.31030728810.221100
2.63-2.843.60.1734952426790.173100
2.84-3.113.50.1395883924980.139100
3.11-3.483.50.1225.2788822370.12299.9
3.48-4.023.40.1016.3683019980.101100
4.02-4.923.30.1155554417010.115100
4.92-6.963.60.1075.2474013110.107100
6.96-45.8353.50.0896.126237510.08999.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 36.13 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å45.83 Å
Translation2.5 Å45.83 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3E8T

3e8t


Resolution: 2.191→45.8 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.875 / WRfactor Rfree: 0.2796 / WRfactor Rwork: 0.1899 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7827 / SU B: 11.732 / SU ML: 0.145 / SU R Cruickshank DPI: 0.0665 / SU Rfree: 0.0538 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1051 4.7 %RANDOM
Rwork0.1938 ---
all0.1975 22345 --
obs0.1975 22345 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.58 Å2 / Biso mean: 28.5456 Å2 / Biso min: 8.96 Å2
Baniso -1Baniso -2Baniso -3
1--21.62 Å20 Å20.24 Å2
2---21.37 Å20 Å2
3---42.98 Å2
Refinement stepCycle: LAST / Resolution: 2.191→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3438 0 64 103 3605
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.023566
X-RAY DIFFRACTIONr_angle_refined_deg1.8531.9734790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.265436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.78526.316152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.98215654
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.73152
X-RAY DIFFRACTIONr_chiral_restr0.1130.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212578
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1719 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.30.5
MEDIUM THERMAL1.922
LS refinement shellResolution: 2.191→2.248 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.454 72 -
Rwork0.319 1291 -
all-1363 -
obs-1363 83.11 %
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)
10.467-0.2251-0.1030.93990.42660.3498-0.01060.04190.0825-0.03630.0055-0.00950.05730.03710.00510.13080.0054-0.03370.09830.01710.02928.348-6.44313.625
20.34750.14440.09280.83360.3620.2362-0.0125-0.0199-0.0432-0.00070.0059-0.0115-0.03270.00180.00660.13170.0089-0.0370.10240.0120.018731.317-20.87330.753
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 220
2X-RAY DIFFRACTION2B2 - 220

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