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- PDB-6jpm: Crystal Structure of Odorant Binding Protein 4 in the Natural Pre... -

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Basic information

Entry
Database: PDB / ID: 6jpm
TitleCrystal Structure of Odorant Binding Protein 4 in the Natural Predator Chrysopa pallens
ComponentsOdorant binding protein 4
KeywordsSTRUCTURAL PROTEIN / Chrysopa pallens (Rambur) / odorant binding protein 4
Function / homologyInsect pheromone/odorant binding protein domains. / Pheromone/general odorant binding protein / PBP/GOBP family / Pheromone/general odorant binding protein superfamily / odorant binding / Odorant binding protein 4
Function and homology information
Biological speciesChrysopa pallens (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.098 Å
AuthorsLi, T.T. / Ma, C.
CitationJournal: Int.J.Biol.Macromol. / Year: 2019
Title: Crystal structure and ligand identification of odorant binding protein 4 in the natural predator Chrysopa pallens.
Authors: Li, T.T. / Liu, W.C. / Zhu, J. / Yang, Y.H. / Ma, C. / Lu, C. / Zhang, K.X.
History
DepositionMar 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Odorant binding protein 4
B: Odorant binding protein 4


Theoretical massNumber of molelcules
Total (without water)27,4662
Polymers27,4662
Non-polymers00
Water2,198122
1
A: Odorant binding protein 4


Theoretical massNumber of molelcules
Total (without water)13,7331
Polymers13,7331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Odorant binding protein 4


Theoretical massNumber of molelcules
Total (without water)13,7331
Polymers13,7331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.745, 135.745, 29.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Odorant binding protein 4


Mass: 13733.067 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chrysopa pallens (insect) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: A0A0R8PDN4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.49 Å3/Da / Density % sol: 50.67 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30%(V/V) 2-propanol, 100mM Tris pH 7.5, 33%(W/V) PEG3350

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.098→47.993 Å / Num. obs: 16276 / % possible obs: 99.3 % / Redundancy: 6.3 % / Net I/σ(I): 8.1
Reflection shellResolution: 2.098→2.16 Å / % possible all: 94

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Processing

Software
NameVersionClassification
PHENIX(1.14rc3_3206: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.098→47.993 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.65
RfactorNum. reflection% reflection
Rfree0.2198 802 4.93 %
Rwork0.1818 --
obs0.1835 16266 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.098→47.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1892 0 0 122 2014
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151928
X-RAY DIFFRACTIONf_angle_d1.0072582
X-RAY DIFFRACTIONf_dihedral_angle_d21.192788
X-RAY DIFFRACTIONf_chiral_restr0.064280
X-RAY DIFFRACTIONf_plane_restr0.006328
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.098-2.22950.26741500.21032440X-RAY DIFFRACTION97
2.2295-2.40160.21231420.19422555X-RAY DIFFRACTION100
2.4016-2.64330.2671340.20042584X-RAY DIFFRACTION100
2.6433-3.02570.22781380.18862564X-RAY DIFFRACTION100
3.0257-3.81190.21161230.17742594X-RAY DIFFRACTION100
3.8119-48.00560.19471150.16872727X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -40.6816 Å / Origin y: -4.8024 Å / Origin z: -9.0575 Å
111213212223313233
T0.2541 Å2-0.0017 Å20.0409 Å2-0.2159 Å2-0.0175 Å2--0.2525 Å2
L2.5762 °2-0.8268 °2-0.9669 °2-0.8679 °20.4178 °2--1.7629 °2
S0.1876 Å °-0.0578 Å °0.4691 Å °-0.0525 Å °-0.0194 Å °-0.1051 Å °-0.3632 Å °-0.0246 Å °-0.1457 Å °
Refinement TLS groupSelection details: all

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