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- PDB-4kyn: Crystal structure of odorant binding protein 48 from Anopheles ga... -

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Basic information

Entry
Database: PDB / ID: 4kyn
TitleCrystal structure of odorant binding protein 48 from Anopheles gambiae at 3.3 Angstrom resolution
ComponentsOdorant binding protein-8
KeywordsTRANSPORT PROTEIN / insect odorant binding protein / OBP48 / olfaction / Anopheles gambiae
Function / homologyRecoverin; domain 1 - #270 / : / : / AgamOBP47-like / Recoverin; domain 1 / Orthogonal Bundle / extracellular region / Mainly Alpha / Odorant binding protein-8
Function and homology information
Biological speciesAnopheles gambiae (African malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.3 Å
AuthorsTsitsanou, K.E. / Drakou, C.E. / Zographos, S.E.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Crystal and Solution Studies of the "Plus-C" Odorant-binding Protein 48 from Anopheles gambiae: CONTROL OF BINDING SPECIFICITY THROUGH THREE-DIMENSIONAL DOMAIN SWAPPING.
Authors: Tsitsanou, K.E. / Drakou, C.E. / Thireou, T. / Vitlin Gruber, A. / Kythreoti, G. / Azem, A. / Fessas, D. / Eliopoulos, E. / Iatrou, K. / Zographos, S.E.
History
DepositionMay 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 20, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Odorant binding protein-8
B: Odorant binding protein-8
C: Odorant binding protein-8
D: Odorant binding protein-8


Theoretical massNumber of molelcules
Total (without water)76,1654
Polymers76,1654
Non-polymers00
Water00
1
A: Odorant binding protein-8
C: Odorant binding protein-8


Theoretical massNumber of molelcules
Total (without water)38,0832
Polymers38,0832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-28 kcal/mol
Surface area16860 Å2
MethodPISA
2
B: Odorant binding protein-8
D: Odorant binding protein-8


Theoretical massNumber of molelcules
Total (without water)38,0832
Polymers38,0832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-25 kcal/mol
Surface area16940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.800, 52.800, 247.860
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Odorant binding protein-8


Mass: 19041.273 Da / Num. of mol.: 4 / Fragment: UNP residues 29-200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles gambiae (African malaria mosquito)
Gene: agamobp48, OBP-8 / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B(DE3) / References: UniProt: Q8MMI9
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: 2.62 Å3/Da / Density % sol: 53.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 4.0 M sodium formate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 23, 2013
Details: 1st mirror: Rh-coated Si mirror, bent for vertical collimation; 2nd mirror: Rh-coated toroidal Si mirror
RadiationMonochromator: double crystal Si(111), first crystal indirectly water-cooled
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.5
ReflectionResolution: 3.3→45.73 Å / Num. all: 11617 / Num. obs: 11606 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 52.01 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 6.7
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 4 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1661 / Rsym value: 0.477 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4IJ7

4ij7


Resolution: 3.3→44.967 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 1.98 / Phase error: 23.9 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.243 554 4.79 %RANDOM
Rwork0.2092 ---
all0.2104 11590 --
obs0.2092 11573 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.83 Å2 / Biso mean: 53.7713 Å2 / Biso min: 19.17 Å2
Refine analyzeLuzzati coordinate error obs: 0.718 Å
Refinement stepCycle: LAST / Resolution: 3.3→44.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5224 0 0 0 5224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015340
X-RAY DIFFRACTIONf_angle_d1.4757140
X-RAY DIFFRACTIONf_chiral_restr0.064760
X-RAY DIFFRACTIONf_plane_restr0.007948
X-RAY DIFFRACTIONf_dihedral_angle_d14.7942088
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3-3.63330.28951250.20582733285896
3.6333-4.15860.23481580.19282767292595
4.1586-5.23750.22471260.19322766289296
5.2375-40.01040.2311450.23722747289295

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