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- PDB-7e8l: The structure of Spodoptera litura chemosensory protein -

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Basic information

Entry
Database: PDB / ID: 7e8l
TitleThe structure of Spodoptera litura chemosensory protein
ComponentsPutative chemosensory protein CSP8
KeywordsSTRUCTURAL PROTEIN / chemosensory protein / alpha-helical protein
Function / homologyInsect odorant-binding protein A10/Ejaculatory bulb-specific protein 3 / Insect odorant-binding protein A10/Ejaculatory bulb-specific protein 3 superfamily / Insect pheromone-binding family, A10/OS-D / Putative chemosensory protein CSP8
Function and homology information
Biological speciesSpodoptera litura (butterflies/moths)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsXie, W. / Jia, Q. / Zeng, H. / Xiao, N. / Tang, J. / Gao, S. / Zhang, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870782 China
CitationJournal: Insects / Year: 2021
Title: The Crystal Structure of the Spodoptera litura Chemosensory Protein CSP8.
Authors: Jia, Q. / Zeng, H. / Zhang, J. / Gao, S. / Xiao, N. / Tang, J. / Dong, X. / Xie, W.
History
DepositionMar 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 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: Putative chemosensory protein CSP8


Theoretical massNumber of molelcules
Total (without water)13,9981
Polymers13,9981
Non-polymers00
Water95553
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.400, 50.055, 60.238
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 Putative chemosensory protein CSP8


Mass: 13997.666 Da / Num. of mol.: 1 / Mutation: E17V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spodoptera litura (butterflies/moths) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0P0EUM0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.07 Å3/Da / Density % sol: 40.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 5.5 / Details: 3M (NH4)2SO4, 0.1M NaOAc pH5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Nov 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→23.7 Å / Num. obs: 5508 / % possible obs: 99.7 % / Redundancy: 4.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Net I/σ(I): 17.9
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 6.4 / Num. unique obs: 776 / CC1/2: 0.958 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1n8u

1n8u


Resolution: 2.3→23.71 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.901 / SU B: 7.976 / SU ML: 0.195 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.432 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2607 266 4.9 %RANDOM
Rwork0.2083 ---
obs0.2108 5212 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.27 Å2 / Biso mean: 26.498 Å2 / Biso min: 12.36 Å2
Baniso -1Baniso -2Baniso -3
1-2.33 Å2-0 Å2-0 Å2
2---1.06 Å20 Å2
3----1.27 Å2
Refinement stepCycle: final / Resolution: 2.3→23.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms935 0 0 53 988
Biso mean---31.35 -
Num. residues----119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.013954
X-RAY DIFFRACTIONr_bond_other_d0.0020.017822
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.6421291
X-RAY DIFFRACTIONr_angle_other_deg1.4831.591910
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1325118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.37523.63655
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.44815164
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.529155
X-RAY DIFFRACTIONr_chiral_restr0.0640.2127
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021079
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02188
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 25 -
Rwork0.194 357 -
all-382 -
obs--97.7 %

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