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- PDB-4ij7: Crystal structure of Odorant Binding Protein 48 from Anopheles ga... -

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Basic information

Entry
Database: PDB / ID: 4ij7
TitleCrystal structure of Odorant Binding Protein 48 from Anopheles gambiae (AgamOBP48) with PEG
ComponentsOdorant binding protein-8
KeywordsTRANSPORT PROTEIN / insect odorant binding protein / OBP48 / olfaction
Function / homologyRecoverin; domain 1 - #270 / : / AgamOBP47-like / Recoverin; domain 1 / Orthogonal Bundle / Mainly Alpha / Odorant binding protein-8
Function and homology information
Biological speciesAnopheles gambiae (African malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsZographos, S.E. / Tsitsanou, K.E. / Drakou, C.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
DepositionDec 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Dec 11, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Odorant binding protein-8
B: Odorant binding protein-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,46510
Polymers38,0832
Non-polymers1,3828
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6450 Å2
ΔGint-116 kcal/mol
Surface area15770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.650, 89.110, 43.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Odorant binding protein-8


Mass: 19041.273 Da / Num. of mol.: 2 / 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
#2: Chemical ChemComp-PEU / 2,5,8,11,14,17,20,23,26,29,32,35,38,41,44,47,50,53,56,59,62,65,68,71,74,77,80-HEPTACOSAOXADOOCTACONTAN-82-OL / PEG 8000


Mass: 1221.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H112O28 / Comment: precipitant*YM
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#4: 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 39.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris-HCl, 25% w/v PEG3000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1.07 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 11, 2011
RadiationMonochromator: Double crystal Si(111), horizontally focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2.25→38.22 Å / Num. all: 15437 / Num. obs: 15437 / % possible obs: 99.95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 18.6
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 4.4 / Num. unique all: 2206 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PM2

3pm2


Resolution: 2.25→38.218 Å / SU ML: 0.26 / σ(F): 0 / Phase error: 24.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2455 768 4.98 %RANDOM
Rwork0.1984 ---
all0.2008 15437 --
obs0.2008 15437 99.95 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 24.725 Å2 / ksol: 0.341 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.8497 Å2-0 Å2-0 Å2
2---1.044 Å20 Å2
3----1.8057 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 2.25→38.218 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2612 0 23 133 2768
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112694
X-RAY DIFFRACTIONf_angle_d1.1533586
X-RAY DIFFRACTIONf_dihedral_angle_d14.4251057
X-RAY DIFFRACTIONf_chiral_restr0.077380
X-RAY DIFFRACTIONf_plane_restr0.006474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.42370.32341320.25572898X-RAY DIFFRACTION100
2.4237-2.66760.29491690.2292847X-RAY DIFFRACTION100
2.6676-3.05340.26661570.21822905X-RAY DIFFRACTION100
3.0534-3.84640.22741680.17932928X-RAY DIFFRACTION100
3.8464-38.22330.20441420.17523091X-RAY DIFFRACTION100

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