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- PDB-4pt1: Crystal structure of Locusta migratoria odorant binding proteins ... -

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Basic information

Entry
Database: PDB / ID: 4pt1
TitleCrystal structure of Locusta migratoria odorant binding proteins lmigOBP1
ComponentsOdorant-binding protein 1d
KeywordsTRANSPORT PROTEIN / OBP / odorant perception
Function / homology
Function and homology information


odorant binding / sensory perception of smell / extracellular space
Similarity search - Function
Pheromone/general odorant binding protein domain / Insect pheromone/odorant binding protein domains. / Pheromone/general odorant binding protein / PBP/GOBP family / Pheromone/general odorant binding protein superfamily / Recoverin; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Odorant-binding protein 1d
Similarity search - Component
Biological speciesLocusta migratoria (migratory locust)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsZheng, J. / Li, J. / Chen, Z.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2015
Title: Crystal structure of the Locusta migratoria odorant binding protein.
Authors: Zheng, J. / Li, J. / Han, L. / Wang, Y. / Wu, W. / Qi, X. / Tao, Y. / Zhang, L. / Zhang, Z. / Chen, Z.
History
DepositionMar 10, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Odorant-binding protein 1d
B: Odorant-binding protein 1d
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4586
Polymers29,9782
Non-polymers4814
Water2,756153
1
A: Odorant-binding protein 1d
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2293
Polymers14,9891
Non-polymers2402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Odorant-binding protein 1d
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2293
Polymers14,9891
Non-polymers2402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.103, 66.039, 51.134
Angle α, β, γ (deg.)90.00, 92.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Odorant-binding protein 1d


Mass: 14988.765 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Locusta migratoria (migratory locust) / Gene: lmigobp1 / Plasmid: pet-22b / Production host: Escherichia coli (E. coli) / References: UniProt: Q3HM32
#2: Chemical
ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 3

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Sample preparation

CrystalDensity Matthews: 1.86 Å3/Da / Density % sol: 33.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6
Details: 25% PEG 3350, pH 6, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 26355 / Num. obs: 23722 / % possible obs: 90 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 1.65→1.68 Å / % possible all: 51

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.383 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.279 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22906 1176 5 %RANDOM
Rwork0.18364 ---
obs0.18592 22536 89.9 %-
all-23722 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.379 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å20.59 Å2
2---1.85 Å20 Å2
3---1.18 Å2
Refinement stepCycle: LAST / Resolution: 1.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1982 0 26 153 2161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022078
X-RAY DIFFRACTIONr_bond_other_d0.0010.021367
X-RAY DIFFRACTIONr_angle_refined_deg1.3051.9472811
X-RAY DIFFRACTIONr_angle_other_deg0.9753.0073339
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0475262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.40525.05101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.42415340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.066158
X-RAY DIFFRACTIONr_chiral_restr0.0820.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022321
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02395
X-RAY DIFFRACTIONr_rigid_bond_restr2.60133441
X-RAY DIFFRACTIONr_sphericity_free21.113557
X-RAY DIFFRACTIONr_sphericity_bonded7.04453491
LS refinement shellResolution: 1.653→1.696 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 47 -
Rwork0.21 898 -
obs--50.32 %

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