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- PDB-3qme: Crystal Structure of an Anopheles gambiae Odorant-binding Protein... -

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Basic information

Entry
Database: PDB / ID: 3qme
TitleCrystal Structure of an Anopheles gambiae Odorant-binding Protein AgamOBP22a with Bound Odorant Cyclohexanone
ComponentsOdorant binding protein (AGAP010409-PA)
KeywordsTRANSPORT PROTEIN / six alpha helix / three disulfate bonds / Odorant-binding protein / mosquito / Cyclohexanone
Function / homology
Function and homology information


odorant binding / response to stimulus / 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
CYCLOHEXANONE / AMMONIUM ION / AGAP010409-PA
Similarity search - Component
Biological speciesAnopheles gambiae (African malaria mosquito)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.002 Å
AuthorsRen, H. / Zhang, S.
CitationJournal: To be Published
Title: Crystal Structures of an Anopheles gambiae Odorant-binding Protein AgamOBP22a and Complexes with Bound Odorants
Authors: Ren, H. / Yang, G. / Winberg, G. / Turin, L. / Zhang, S.
History
DepositionFeb 4, 2011Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 23, 2011ID: 3L5G
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.4Sep 13, 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 / pdbx_initial_refinement_model / 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 (AGAP010409-PA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2146
Polymers16,0431
Non-polymers1705
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.986, 37.593, 43.618
Angle α, β, γ (deg.)90.00, 99.17, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-246-

HOH

21A-257-

HOH

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Components

#1: Protein Odorant binding protein (AGAP010409-PA) / Odorant-binding protein OBPjj83b


Mass: 16043.329 Da / Num. of mol.: 1 / Fragment: AgamOBP22a, UNP residues 22-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles gambiae (African malaria mosquito)
Strain: PEST / Gene: AgamOBP22a, AGAP010409, OBP22, OBPjj83b / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-STAR-pLysS / References: UniProt: Q7PGA3
#2: Chemical ChemComp-CYH / CYCLOHEXANONE


Mass: 98.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10O
#3: Chemical
ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H4N
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O

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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: 1.82 Å3/Da / Density % sol: 32.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Ammonium citrate tribasic, MPD, pH 7.0, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 7597 / % possible obs: 96.1 % / Redundancy: 7 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 14.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2-2.0370.28593.6
2.03-2.076.90.393.5
2.07-2.116.90.24493.9
2.11-2.157.10.21194.3
2.15-2.270.20195.5
2.2-2.257.10.18394.4
2.25-2.317.10.1694.8
2.31-2.377.10.14995.2
2.37-2.447.10.13895
2.44-2.527.10.1396
2.52-2.6170.11196.6
2.61-2.717.20.09996.5
2.71-2.847.10.09196.8
2.84-2.997.10.07697.2
2.99-3.177.10.06297.8
3.17-3.4270.04997.7
3.42-3.767.10.04197.8
3.76-4.3170.03498.5
4.31-5.4270.03398.8
5.42-306.60.03898.1

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L4A

3l4a


Resolution: 2.002→25.487 Å / Occupancy max: 1 / Occupancy min: 0.42 / SU ML: 0.22 / σ(F): 0 / Phase error: 21.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2107 764 10.22 %
Rwork0.169 --
obs0.1733 7478 94.45 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.14 Å2 / ksol: 0.356 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.628 Å2-0 Å21.6466 Å2
2--1.3055 Å20 Å2
3----1.9335 Å2
Refinement stepCycle: LAST / Resolution: 2.002→25.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms961 0 11 69 1041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071016
X-RAY DIFFRACTIONf_angle_d0.9311376
X-RAY DIFFRACTIONf_dihedral_angle_d14.452380
X-RAY DIFFRACTIONf_chiral_restr0.073142
X-RAY DIFFRACTIONf_plane_restr0.003189
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0021-2.15660.25671460.17251255X-RAY DIFFRACTION89
2.1566-2.37350.25931550.17211307X-RAY DIFFRACTION93
2.3735-2.71660.24771480.17291344X-RAY DIFFRACTION95
2.7166-3.42130.18831550.17181374X-RAY DIFFRACTION97
3.4213-25.48870.18221600.16361434X-RAY DIFFRACTION98

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