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- PDB-3l4a: Crystal Structure of an Anopheles gambiae Odorant-binding Protein 22a -

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Basic information

Entry
Database: PDB / ID: 3l4a
TitleCrystal Structure of an Anopheles gambiae Odorant-binding Protein 22a
ComponentsOdorant binding protein (AGAP010409-PA)
KeywordsTRANSPORT PROTEIN / all alpha helix
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
AMMONIUM ION / AGAP010409-PA
Similarity search - Component
Biological speciesAnopheles gambiae (African malaria mosquito)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsRen, H. / Zhang, S.
CitationJournal: To be Published
Title: The Crystal Structure 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
Revision 1.5Sep 6, 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
Revision 1.6Nov 6, 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 (AGAP010409-PA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,28010
Polymers16,0431
Non-polymers2369
Water2,324129
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.194, 37.729, 43.703
Angle α, β, γ (deg.)90.00, 99.29, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-220-

HOH

21A-223-

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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: H4N
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 1.83 Å3/Da / Density % sol: 32.81 %
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 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 17623 / % possible obs: 94 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 38.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
1.5-1.533.10.18182.8
1.53-1.553.10.15885.4
1.55-1.583.20.15184.9
1.58-1.623.20.13287.9
1.62-1.653.30.12188.7
1.65-1.693.30.10490
1.69-1.733.40.09391.4
1.73-1.783.40.08592.2
1.78-1.833.50.07293.5
1.83-1.893.60.06694.1
1.89-1.963.60.05594.6
1.96-2.043.60.04896.3
2.04-2.133.90.04697.3
2.13-2.244.10.042100
2.24-2.384.30.041100
2.38-2.564.60.041100
2.56-2.8250.04100
2.82-3.235.90.04100
3.23-4.077.10.031100
4.07-306.90.02699.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L47

3l47


Resolution: 1.5→25.465 Å / Occupancy max: 1 / Occupancy min: 0.19 / SU ML: 1.31 / σ(F): 0.06 / Phase error: 20.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2067 1028 5.92 %
Rwork0.1768 --
obs0.1786 17369 92.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.58 Å2 / ksol: 0.381 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0122 Å20 Å20.9708 Å2
2--0.5121 Å2-0 Å2
3----0.5242 Å2
Refinement stepCycle: LAST / Resolution: 1.5→25.465 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms977 0 14 129 1120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051064
X-RAY DIFFRACTIONf_angle_d0.8461449
X-RAY DIFFRACTIONf_dihedral_angle_d19.203398
X-RAY DIFFRACTIONf_chiral_restr0.07153
X-RAY DIFFRACTIONf_plane_restr0.003199
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5002-1.57930.24821320.20531996X-RAY DIFFRACTION80
1.5793-1.67830.22511200.18932168X-RAY DIFFRACTION86
1.6783-1.80780.23681300.18092271X-RAY DIFFRACTION90
1.8078-1.98970.22941460.18892362X-RAY DIFFRACTION94
1.9897-2.27740.22271750.17292437X-RAY DIFFRACTION98
2.2774-2.86870.21661750.17372506X-RAY DIFFRACTION100
2.8687-25.46830.17351500.16772601X-RAY DIFFRACTION100

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