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- PDB-6vq5: Crystal Structure of Epiphyas postvittana Pheromone Binding Protein 3 -

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Basic information

Entry
Database: PDB / ID: 6vq5
TitleCrystal Structure of Epiphyas postvittana Pheromone Binding Protein 3
ComponentsPheromome Binding Protein
KeywordsTRANSPORT PROTEIN / Insect Pheromone Binding Protein / Insect Odorant Binding Protein
Function / homologyOdorant/pheromone binding protein, Lepidoptera / Insect pheromone/odorant binding protein domains. / Pheromone/general odorant binding protein / PBP/GOBP family / Pheromone/general odorant binding protein superfamily / odorant binding / Pheromome Binding Protein
Function and homology information
Biological speciesEpiphyas postvittana (butterflies/moths)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsHamiaux, C. / Carraher, C.
CitationJournal: Sci Rep / Year: 2020
Title: Crystal structure of Epiphyas postvittana pheromone binding protein 3.
Authors: Hamiaux, C. / Carraher, C. / Lofstedt, C. / Corcoran, J.A.
History
DepositionFeb 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / 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
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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pheromome Binding Protein
B: Pheromome Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8524
Polymers36,6122
Non-polymers2402
Water1629
1
A: Pheromome Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5463
Polymers18,3061
Non-polymers2402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Pheromome Binding Protein


Theoretical massNumber of molelcules
Total (without water)18,3061
Polymers18,3061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.379, 53.379, 105.949
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 12 - 128 / Label seq-ID: 12 - 128

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

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Components

#1: Protein Pheromome Binding Protein


Mass: 18305.830 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Epiphyas postvittana (butterflies/moths)
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A0K8TU48
#2: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 40.61 % / Description: Rods
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES pH 6.5 12 % PEG 20K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.6→47.67 Å / Num. obs: 9187 / % possible obs: 100 % / Redundancy: 14.2 % / Biso Wilson estimate: 72.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.031 / Rrim(I) all: 0.117 / Net I/σ(I): 12.4
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 14.7 % / Rmerge(I) obs: 2.249 / Num. measured all: 16455 / Num. unique obs: 1116 / CC1/2: 0.644 / Rpim(I) all: 0.602 / Rrim(I) all: 2.329 / Net I/σ(I) obs: 1.5 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.3data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DQE

1dqe


Resolution: 2.6→47.66 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.931 / SU B: 30.13 / SU ML: 0.285 / SU R Cruickshank DPI: 0.7092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.709 / ESU R Free: 0.318
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2589 505 5.5 %RANDOM
Rwork0.2161 ---
obs0.2183 8653 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 157.1 Å2 / Biso mean: 84.003 Å2 / Biso min: 56.64 Å2
Baniso -1Baniso -2Baniso -3
1-2.03 Å20 Å20 Å2
2--2.03 Å20 Å2
3----4.05 Å2
Refinement stepCycle: final / Resolution: 2.6→47.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1835 0 16 9 1860
Biso mean--119.93 72.94 -
Num. residues----230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0131882
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171785
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.6222525
X-RAY DIFFRACTIONr_angle_other_deg1.2221.5874163
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1165227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57425.38591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.28715369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.584154
X-RAY DIFFRACTIONr_chiral_restr0.0610.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022029
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02339
Refine LS restraints NCS

Ens-ID: 1 / Number: 3531 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 34 -
Rwork0.335 651 -
all-685 -
obs--100 %
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)
17.363-0.02-1.85272.7762-0.27664.98150.10940.8275-0.3023-0.5253-0.10410.5371-0.0513-1.0628-0.00530.22170.0219-0.10230.3038-0.04590.116532.66654.93553.823
22.64951.67620.36845.6390.45365.81990.1493-0.394-0.39310.46370.00090.05730.9313-0.0002-0.15020.27160.0432-0.02250.12540.07360.081747.67232.97852.741
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 128
2X-RAY DIFFRACTION2B12 - 128

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