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- PDB-3vb1: Crystal Structure of Anopholes gambiae odorant binding protein 20... -

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Basic information

Entry
Database: PDB / ID: 3vb1
TitleCrystal Structure of Anopholes gambiae odorant binding protein 20 in open state
ComponentsAGAP005208-PA
KeywordsODORANT-BINDING PROTEIN / insect odorant binding protein / odor transport / possible odorant receptor / None / secreted lymph olfactory sensillum
Function / homology
Function and homology information


dibutyl phthalate binding / olfactory behavior / odorant binding / sensory perception of smell / extracellular region
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
ACETIC ACID / AGAP005208-PA
Similarity search - Component
Biological speciesAnopheles gambiae (African malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsZiemba, B.P. / Jones, D.N.
CitationJournal: Protein Sci. / Year: 2013
Title: A novel mechanism of ligand binding and release in the odorant binding protein 20 from the malaria mosquito Anopheles gambiae.
Authors: Ziemba, B.P. / Murphy, E.J. / Edlin, H.T. / Jones, D.N.
History
DepositionDec 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2012Group: Database references
Revision 1.2Dec 26, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
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_conn / 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_conn.pdbx_leaving_atom_flag / _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: AGAP005208-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5272
Polymers13,4671
Non-polymers601
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.923, 36.463, 92.091
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AGAP005208-PA


Mass: 13466.953 Da / Num. of mol.: 1 / Fragment: UNP Residues 24-142
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles gambiae (African malaria mosquito)
Gene: OBP20, AgaP_AGAP005208 / Plasmid: pET13a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q7Q9J3
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.18 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 276 K / Method: vapor diffusion, hanging drop / pH: 5.57
Details: 1.9 M ammonium sulfate, 0.2 M potassium sodium tartrate, 0.1 M sodium citrate, pH 5.57, VAPOR DIFFUSION, HANGING DROP, temperature 276K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: May 12, 2007
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→33.9 Å / Num. all: 9029 / Num. obs: 9029 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.41 % / Rmerge(I) obs: 0.046 / Χ2: 0.94 / Net I/σ(I): 15.8 / Scaling rejects: 813
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.95-2.024.530.1985.540958931.1100
2.02-2.14.390.1568.440198661.4499.7
2.1-2.24.570.1119.541458970.9699.9
2.2-2.313.990.1612.938588791.5798.8
2.31-2.464.570.0713.340218750.7899.9
2.46-2.654.570.06213.641278990.76100
2.65-2.914.590.0561642029110.71100
2.91-3.334.520.04819.440999030.6799.9
3.33-4.24.240.04521.339549170.7298.6
4.2-33.94.130.02636.841139890.8199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å34.92 Å
Translation2.5 Å34.92 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.7Ldata scaling
d*TREK9.7Ldata reduction
PHASER1.3.3phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
JBluIce-EPICSdata collection
Blu-IceICEdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3V2L

3v2l


Resolution: 2→32.65 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.2737 / WRfactor Rwork: 0.2293 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.7821 / SU B: 13.617 / SU ML: 0.17 / SU R Cruickshank DPI: 0.2745 / SU Rfree: 0.2123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.275 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2711 828 9.9 %RANDOM
Rwork0.2306 ---
all0.2348 8348 --
obs0.2348 8348 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 74.79 Å2 / Biso mean: 38.4144 Å2 / Biso min: 15.69 Å2
Baniso -1Baniso -2Baniso -3
1--2.73 Å20 Å20 Å2
2--3.58 Å20 Å2
3----0.84 Å2
Refinement stepCycle: LAST / Resolution: 2→32.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms920 0 4 67 991
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221016
X-RAY DIFFRACTIONr_bond_other_d0.0010.02689
X-RAY DIFFRACTIONr_angle_refined_deg1.3831.9941372
X-RAY DIFFRACTIONr_angle_other_deg0.89831701
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0485133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.27525.7540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.28815197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.348155
X-RAY DIFFRACTIONr_chiral_restr0.0820.2157
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021133
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02180
X-RAY DIFFRACTIONr_mcbond_it0.9671.5655
X-RAY DIFFRACTIONr_mcbond_other0.3191.5261
X-RAY DIFFRACTIONr_mcangle_it1.56821056
X-RAY DIFFRACTIONr_scbond_it2.9993361
X-RAY DIFFRACTIONr_scangle_it4.1834.5316
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 63 -
Rwork0.268 554 -
all-617 -
obs--99.2 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
122.2629-12.5028-10.445820.12935.01494.96640.1432-0.3985-0.2207-0.55-0.2702-0.8515-0.01420.17010.1270.4572-0.12320.14420.2979-0.03130.394-4.70348.848328.5843
24.70371.3301-2.02375.0148-1.28384.444-0.2721-0.5399-0.13960.2730.19120.44690.07720.33990.0810.11340.07990.03180.17820.11320.12198.84336.232114.9233
34.4832-3.038-1.2155.0053-1.35164.318-0.2282-0.6893-0.07280.74190.1276-0.2016-0.1887-0.00940.10060.2078-0.0424-0.0320.3179-0.03490.1659-8.907710.231612.5629
411.2931-0.94110.96842.5394-0.8293.4352-0.1989-0.38030.06560.0961-0.1196-0.088-0.0412-0.20560.31850.0685-0.01330.00110.0573-0.01430.0311.86229.19675.4225
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 9
2X-RAY DIFFRACTION2A10 - 60
3X-RAY DIFFRACTION3A61 - 83
4X-RAY DIFFRACTION4A84 - 120

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