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- PDB-5dic: Fatty acid binding protein OBP56a from the oral disk of the blowf... -

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Basic information

Entry
Database: PDB / ID: 5dic
TitleFatty acid binding protein OBP56a from the oral disk of the blowfly Phormia regina
ComponentsOdorant-binding protein
KeywordsOdorant-binding protein / Palmitate olfaction odorant
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
PALMITIC ACID / Odorant-binding protein
Similarity search - Component
Biological speciesPhormia regina (black blowfly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.185 Å
AuthorsIshida, Y. / Leal, W.S. / Wilson, D.K.
CitationJournal: To Be Published
Title: In preparation
Authors: Ishida, Y. / Leal, W.S. / Wilson, D.K.
History
DepositionAug 31, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Odorant-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7893
Polymers13,2761
Non-polymers5132
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint2 kcal/mol
Surface area6920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.845, 33.800, 35.399
Angle α, β, γ (deg.)105.35, 106.44, 113.12
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Odorant-binding protein


Mass: 13276.255 Da / Num. of mol.: 1 / Fragment: UNP residues 19-135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phormia regina (black blowfly) / Gene: PregOBP56a / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: L8B8J6
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 20% PEG 6000, 1M LiCl, 100mM citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.18→28.1 Å / Num. obs: 34518 / % possible obs: 87.4 % / Redundancy: 2.48 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 9.3
Reflection shellResolution: 1.18→1.22 Å / Rmerge(I) obs: 0.176

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 1.185→28.1 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.003 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16783 1674 5 %RANDOM
Rwork0.13101 ---
obs0.13286 31884 85.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.525 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20.56 Å20.22 Å2
2--0.16 Å20.4 Å2
3----0.83 Å2
Refinement stepCycle: 1 / Resolution: 1.185→28.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms913 0 36 133 1082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.019964
X-RAY DIFFRACTIONr_bond_other_d0.0010.02970
X-RAY DIFFRACTIONr_angle_refined_deg1.4812.0011277
X-RAY DIFFRACTIONr_angle_other_deg0.82132271
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2265114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.7326.27943
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.84615190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.311152
X-RAY DIFFRACTIONr_chiral_restr0.0970.2135
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021029
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02187
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4041.469459
X-RAY DIFFRACTIONr_mcbond_other1.3631.466458
X-RAY DIFFRACTIONr_mcangle_it1.8322.212572
X-RAY DIFFRACTIONr_mcangle_other1.8372.215573
X-RAY DIFFRACTIONr_scbond_it3.8312.055505
X-RAY DIFFRACTIONr_scbond_other3.8272.057506
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8982.882706
X-RAY DIFFRACTIONr_long_range_B_refined3.73913.7141180
X-RAY DIFFRACTIONr_long_range_B_other3.74113.7261181
X-RAY DIFFRACTIONr_rigid_bond_restr2.72731934
X-RAY DIFFRACTIONr_sphericity_free26.735544
X-RAY DIFFRACTIONr_sphericity_bonded10.03452008
LS refinement shellResolution: 1.185→1.216 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.176 74 -
Rwork0.185 1549 -
obs--55.75 %

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