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- PDB-3l47: Crystal Structure of the Anopheles gambiae Odorant-binding Protein 22a -

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Basic information

Entry
Database: PDB / ID: 3l47
TitleCrystal Structure of the Anopheles gambiae Odorant-binding Protein 22a
ComponentsOdorant binding protein (AGAP010409-PA)
KeywordsTRANSPORT PROTEIN / all alpha helix
Function / homology
Function and homology information


odorant binding / response to stimulus / sensory perception of smell
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
Biological speciesAnopheles gambiae (African malaria mosquito)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.506 Å
AuthorsRen, H. / Zhang, S.
CitationJournal: To be Published
Title: The Crystal Structures of an Anopheles gambiae Odorant-binding Protein AgamOBP22a and complexes with bound Odorants
Authors: Ren, H. / Yang, G. / Winberg, G. / Turin, L. / Mershin, A. / Zhang, S.
History
DepositionDec 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Atomic model
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Odorant binding protein (AGAP010409-PA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4373
Polymers16,0431
Non-polymers3942
Water70339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.871, 37.920, 43.889
Angle α, β, γ (deg.)90.000, 98.920, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-174-

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-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Au
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 1.84 Å3/Da / Density % sol: 33.2 %
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: Jun 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 4107 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Rmerge(I) obs: 0.064 / Χ2: 4.192 / Net I/σ(I): 32.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.5-2.546.10.142092.53899.5
2.54-2.5960.1251963100
2.59-2.6460.1082052.712100
2.64-2.696.20.1112033.004100
2.69-2.7560.1052052.969100
2.75-2.826.20.0891883.044100
2.82-2.896.30.0922233.145100
2.89-2.966.20.091883.376100
2.96-3.056.20.0822113.552100
3.05-3.156.30.0732003.23799.5
3.15-3.266.10.0712064.218100
3.26-3.396.30.0642114.06699.5
3.39-3.556.40.0641924.398100
3.55-3.736.20.0532183.99399.5
3.73-3.976.30.0552044.54799.5
3.97-4.276.30.0491984.48899
4.27-4.76.10.052025.1999.5
4.7-5.386.20.0512125.39299.5
5.38-6.766.20.0612147.53699.5
6.76-305.70.0522229.18100

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Phasing

PhasingMethod: SAD
Phasing dmFOM : 0.75 / FOM acentric: 0.77 / FOM centric: 0.55 / Reflection: 4096 / Reflection acentric: 3717 / Reflection centric: 379
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.2-29.8280.860.880.7818914445
4.5-7.20.860.890.6755848375
3.6-4.50.850.880.5969863266
3.1-3.60.790.820.4367962257
2.7-3.10.690.710.481235114392
2.5-2.70.620.630.4273769344

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
RESOLVE2.13phasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.506→29.828 Å / Occupancy max: 1 / Occupancy min: 0.56 / SU ML: 2.11 / σ(F): 0.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.226 408 10.03 %
Rwork0.18 --
obs0.185 4069 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.636 Å2 / ksol: 0.352 e/Å3
Displacement parametersBiso max: 61.74 Å2 / Biso mean: 24.832 Å2 / Biso min: 14.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.466 Å20 Å23.583 Å2
2---1.114 Å20 Å2
3---1.398 Å2
Refinement stepCycle: LAST / Resolution: 2.506→29.828 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms873 0 2 39 914
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01892
X-RAY DIFFRACTIONf_angle_d1.1561204
X-RAY DIFFRACTIONf_chiral_restr0.081127
X-RAY DIFFRACTIONf_plane_restr0.004164
X-RAY DIFFRACTIONf_dihedral_angle_d23.034318
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.506-2.8680.2641330.19511971330139397
2.868-3.6130.2161350.17312111346134699
3.613-29.830.2131400.17612531393133099

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