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- PDB-3pm2: Crystal structure of a novel type of odorant binding protein from... -

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Basic information

Entry
Database: PDB / ID: 3pm2
TitleCrystal structure of a novel type of odorant binding protein from Anopheles gambiae belonging to the c+ class
ComponentsOdorant binding protein (AGAP007287-PA)
KeywordsTRANSPORT PROTEIN / alpha helical protein / odorant binding protein / odorant molecules / antennae
Function / homology
Function and homology information


odorant binding / sensory perception of smell / extracellular region
Similarity search - Function
Recoverin; domain 1 - #270 / : / : / AgamOBP47-like / Pheromone/general odorant binding protein superfamily / Recoverin; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Odorant-binding protein 47
Similarity search - Component
Biological speciesAnopheles gambiae (African malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / remote SAD / Resolution: 1.8 Å
AuthorsSpinelli, S. / Lagarde, A. / Qiao, H. / Tegoni, M. / Pelosi, P. / Cambillau, C.
CitationJournal: Biochem.J. / Year: 2011
Title: Crystal structure of a novel type of odorant-binding protein from Anopheles gambiae, belonging to the C-plus class.
Authors: Lagarde, A. / Spinelli, S. / Qiao, H. / Tegoni, M. / Pelosi, P. / Cambillau, C.
History
DepositionNov 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Database references
Revision 1.3Jun 13, 2018Group: Data collection / Category: diffrn_radiation / Item: _diffrn_radiation.pdbx_diffrn_protocol
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Odorant binding protein (AGAP007287-PA)


Theoretical massNumber of molelcules
Total (without water)18,9641
Polymers18,9641
Non-polymers00
Water5,224290
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.289, 36.289, 263.541
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-201-

HOH

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Components

#1: Protein Odorant binding protein (AGAP007287-PA) / Putative odorant-binding protein OBPjj2


Mass: 18964.145 Da / Num. of mol.: 1 / Fragment: UNP residues 58-228
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles gambiae (African malaria mosquito)
Gene: OBP47, OBPjj2, AGAP007287 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7PF80
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.29 Å3/Da / Density % sol: 46.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Protein 12 mg/ml, 30-35% PEG5000 MME, 0.1 M sodium acetate pH 5.7-6.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF BM1410.97625
SYNCHROTRONSOLEIL PROXIMA 121.7712
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDMay 8, 2010
ADSC QUANTUM 42CCDJun 29, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1mirrorsSINGLE WAVELENGTHMx-ray1
2mirrorsSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.976251
21.77121
ReflectionResolution: 1.8→36.3 Å / Num. all: 17578 / Num. obs: 17578 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.5 % / Biso Wilson estimate: 23.42 Å2 / Rmerge(I) obs: 0.167 / Rsym value: 0.167 / Net I/σ(I): 19.3
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 4 / Rsym value: 0.55 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXDphasing
PHASERphasing
BUSTER2.9.2refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: remote SAD / Resolution: 1.8→34.99 Å / Cor.coef. Fo:Fc: 0.9457 / Cor.coef. Fo:Fc free: 0.9239 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2272 887 5.06 %RANDOM
Rwork0.1868 ---
obs0.1887 17530 --
all-17530 --
Displacement parametersBiso mean: 26.31 Å2
Baniso -1Baniso -2Baniso -3
1--2.225 Å20 Å20 Å2
2---2.225 Å20 Å2
3---4.45 Å2
Refine analyzeLuzzati coordinate error obs: 0.227 Å
Refinement stepCycle: LAST / Resolution: 1.8→34.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1309 0 0 290 1599
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0111343HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.021820HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d462SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct185
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes31HARMONIC2
X-RAY DIFFRACTIONt_gen_planes190HARMONIC5
X-RAY DIFFRACTIONt_it1343HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact
LS refinement shellResolution: 1.8→1.91 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2493 140 5.08 %
Rwork0.2099 2616 -
all0.2118 2756 -
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)
10.02170.83420.21450.3232-0.2220.1082-0.002-0.00790.0098-0.02190.0153-0.0049-0.00840.0148-0.01330.0281-0.0669-0.0560.0061-0.0082-0.030510.921718.012815.2958
20-0.01640.09110.0830.0870-0.00130.00630.0087-0.00930.00840.0121-0.0059-0.0068-0.00710.02440.0112-0.0705-0.01530.0398-0.0027-5.588216.947813.0403
30.33850.72930.32670.65060.11910.19210.0029-0.0110.00790.0131-0.00270.0164-0.00990.0111-0.0003-0.00010.0026-0.0068-0.05570.020.05394.139415.417429.8219
40.28580.08630.20610.40660.32460.14910.0012-0.00590.00790.00340.00120.01340.0035-0.0304-0.0024-0.0393-0.0026-0.0038-0.00980.03420.0434-7.79719.249625.8796
50.66560.68430.8730.1732-0.0120.0791-0.00180.0218-0.0099-0.0091-0.00830.03180.0027-0.01470.0101-0.022-0.0388-0.08220.03860.0234-0.0082-10.33476.12798.7938
600.23070.26790.61870.07180.0666-0.00920.0511-0.05240.00810.017-0.02750.0151-0.0075-0.00780.0178-0.0295-0.0364-0.01350.01250.0115-1.6926-1.100416.41
70.4733-0.1393-0.24250-0.2040.57490.0089-0.04070.01680.0211-0.00180.0402-0.0065-0.0002-0.00720.0114-0.01060.0063-0.0070.01940.0083-0.30978.628732.0025
80.41120.16810.03520.24960.13070.8767-0.0090.00380.0027-0.01910.02530.0265-0.03650.0383-0.01640.0239-0.0853-0.04240.02970.0209-0.06968.236812.06358.1706
Refinement TLS groupSelection details: { A|2 - A|173 }

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