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- PDB-3n7h: Crystal structure of Odorant Binding Protein 1 from Anopheles gam... -

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Basic information

Entry
Database: PDB / ID: 3n7h
TitleCrystal structure of Odorant Binding Protein 1 from Anopheles gambiae (AgamOBP1) with DEET (N,N-Diethyl-meta-toluamide) and PEG
ComponentsOdorant binding proteinOdorant-binding protein
KeywordsTRANSPORT PROTEIN / INSECT ODORANT BINDING PROTEIN / OBP1 / AgamOBP1 / DEET / N / N-Diethyl-meta-toluamide / OLFACTION
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
N,N-diethyl-3-methylbenzamide / METHANOL / Odorant binding protein
Similarity search - Component
Biological speciesAnopheles gambiae (African malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsTsitsanou, K.E. / Zographos, S.E.
CitationJournal: Cell.Mol.Life Sci. / Year: 2012
Title: Anopheles gambiae odorant binding protein crystal complex with the synthetic repellent DEET: implications for structure-based design of novel mosquito repellents.
Authors: Tsitsanou, K.E. / Thireou, T. / Drakou, C.E. / Koussis, K. / Keramioti, M.V. / Leonidas, D.D. / Eliopoulos, E. / Iatrou, K. / Zographos, S.E.
History
DepositionMay 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 18, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _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
B: Odorant binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,29718
Polymers29,0952
Non-polymers3,20116
Water6,287349
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-53 kcal/mol
Surface area12430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.930, 63.540, 68.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Odorant binding protein / Odorant-binding protein


Mass: 14547.619 Da / Num. of mol.: 2 / Fragment: UNP residues 20-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles gambiae (African malaria mosquito)
Gene: AgamOBP1, OBP-1 / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): OrigamiB(DE3) / References: UniProt: Q8T6S0

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Non-polymers , 6 types, 365 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-MOH / METHANOL / Methanol


Mass: 32.042 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH4O
#4: Chemical ChemComp-DE3 / N,N-diethyl-3-methylbenzamide / DEET


Mass: 191.269 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H17NO
#5: 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 / Polyethylene glycol


Mass: 1221.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H112O28 / Comment: precipitant*YM
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.08 Å3/Da / Density % sol: 40.86 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 32% PEG 8000, 250 mM MgCl2, 50 mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.81 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 8, 2010
RadiationMonochromator: Double crystal Si(111), horizontally focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 1.598→63.54 Å / Num. all: 32525 / Num. obs: 32525 / % possible obs: 99.3 % / Redundancy: 5 % / Biso Wilson estimate: 21.5 Å2 / Rsym value: 0.08 / Net I/σ(I): 12.6
Reflection shellResolution: 1.6→1.68 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 4578 / Rsym value: 0.414 / % possible all: 98.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.72 Å31.77 Å
Translation1.72 Å31.77 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
MAR345data collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ERB

2erb


Resolution: 1.6→63.54 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.193 / WRfactor Rwork: 0.166 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.894 / SU B: 3.764 / SU ML: 0.06 / SU R Cruickshank DPI: 0.101 / SU Rfree: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1642 5.1 %RANDOM
Rwork0.172 ---
all0.174 32525 --
obs0.174 32416 98.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 73.12 Å2 / Biso mean: 16.734 Å2 / Biso min: 8.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2--0.35 Å20 Å2
3----0.65 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å
Refinement stepCycle: LAST / Resolution: 1.6→63.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2034 0 76 349 2459
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212343
X-RAY DIFFRACTIONr_angle_refined_deg1.2781.9943181
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2065290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.18725.14107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9815433
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.55156
X-RAY DIFFRACTIONr_chiral_restr0.0910.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211786
X-RAY DIFFRACTIONr_mcbond_it0.3481.51364
X-RAY DIFFRACTIONr_mcangle_it0.69122233
X-RAY DIFFRACTIONr_scbond_it1.4643979
X-RAY DIFFRACTIONr_scangle_it2.4424.5940
LS refinement shellResolution: 1.598→1.639 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 133 -
Rwork0.248 2168 -
all-2301 -
obs--97.62 %
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)
110.58870.2567-11.22891.25895.66430.36191.45451.2348-0.6354-0.5466-0.9720.1054-0.8004-2.7014-0.48250.55440.1774-0.34860.2378-0.03850.18013.9646-8.78895.2032
25.6699-1.03113.3060.7531-1.14635.2219-0.00050.39950.0691-0.3143-0.0974-0.10210.12850.36150.09790.17520.01240.04220.09870.00360.073717.993-11.73468.9312
37.6420.5268-1.30263.8084-1.59494.0903-0.05520.1366-0.1018-0.18050.0933-0.133-0.00170.2291-0.03810.08750.0030.01190.1087-0.0030.09920.9754-14.11822.7282
40.7334-0.28260.16411.5349-0.53542.04780.0030.025-0.0585-0.0538-0.00230.03780.10020.007-0.00070.1097-0.00070.00660.10070.0030.101810.3691-15.14523.7124
53.97630.9823-2.23380.4453-3.18943.7497-0.280.1798-0.1557-0.14920.38190.15740.2909-0.6065-0.10180.1352-0.0336-0.02310.11770.02370.14731.0547-11.76819.2776
61.1150.5651-0.43221.9776-0.44270.8750.0095-0.04010.04030.07370.0099-0.0499-0.03130.056-0.01940.09860.0061-0.0010.1096-0.00350.099116.57-1.737325.516
71.0571-0.9636-0.71021.56251.17191.39010.07210.12510.0326-0.1415-0.0114-0.0203-0.09390.0206-0.06070.1098-0.00660.01020.09320.01350.083614.09773.524511.7374
83.32990.81090.27276.9176-1.24134.92430.0348-0.08070.19120.14240.10180.2758-0.2481-0.1498-0.13660.11580.00860.0230.108-0.00220.10027.86111.394530.7545
90.4134-0.21680.43141.103-0.24721.77220.03080.0230.0262-0.05210.00820.01230.0107-0.0771-0.03890.0922-0.005300.11280.01210.09996.9931-3.676916.2955
101.9453-0.41462.45182.6863-1.3466.83110.06440.1556-0.0601-0.28580.0001-0.12470.08580.0371-0.06450.1361-0.0004-0.00930.095-0.01040.076815.619924.9124-2.8472
110.4413-0.22520.24983.66792.99154.09460.09030.1847-0.0523-0.2985-0.1260.1715-0.2173-0.21810.03570.07640.0356-0.02520.1569-0.00880.08874.624631.72367.7407
122.0442-1.5235-0.073.23622.82186.7329-0.0059-0.13630.06260.0134-0.00240.11150.0477-0.21960.00840.10160.00130.00050.08020.00090.114711.807839.493417.4011
139.40790.8579-2.431314.20623.947112.80350.37250.30460.4993-0.70380.0099-0.0433-0.6206-0.148-0.38240.1387-0.01070.01990.09330.02830.094917.096637.77768.4203
141.4066-0.19740.32541.13310.69390.97830.004-0.0542-0.017-0.02720.00140.0397-0.04650.0381-0.00540.10980.0064-0.00550.1009-0.00270.122414.460729.718116.2277
151.14230.2081-0.2130.82860.12161.339-0.05450.0758-0.0919-0.06210.01070.03340.0908-0.05470.04380.1128-0.0080.00140.0871-0.00730.1168.934215.59610.5503
161.5145-2.1711-0.71346.61891.28540.27-0.0817-0.20870.14620.54640.2405-0.33610.08930.1624-0.15890.12090.0095-0.03730.1158-0.03310.136918.635517.294522.4026
170.4132-0.1592-0.38941.12790.54911.91330.0202-0.0064-0.0331-0.02230.00050.03310.04160.0175-0.02070.0982-0.0002-0.00590.1126-0.00950.11517.956323.653712.655
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 5
2X-RAY DIFFRACTION2A6 - 19
3X-RAY DIFFRACTION3A20 - 26
4X-RAY DIFFRACTION4A27 - 41
5X-RAY DIFFRACTION5A42 - 47
6X-RAY DIFFRACTION6A48 - 75
7X-RAY DIFFRACTION7A76 - 98
8X-RAY DIFFRACTION8A99 - 106
9X-RAY DIFFRACTION9A107 - 125
10X-RAY DIFFRACTION10B1 - 10
11X-RAY DIFFRACTION11B11 - 26
12X-RAY DIFFRACTION12B27 - 33
13X-RAY DIFFRACTION13B34 - 38
14X-RAY DIFFRACTION14B39 - 68
15X-RAY DIFFRACTION15B69 - 94
16X-RAY DIFFRACTION16B95 - 101
17X-RAY DIFFRACTION17B102 - 125

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