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- PDB-3r1o: Odorant Binding Protein 7 from Anopheles gambiae with Four Disulf... -

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Basic information

Entry
Database: PDB / ID: 3r1o
TitleOdorant Binding Protein 7 from Anopheles gambiae with Four Disulfide Bridges
ComponentsOdorant binding protein, antennal
KeywordsTRANSPORT PROTEIN / all helical protein / odorant molecules binding / mosquito antenna
Function / homology
Function and homology information


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
PALMITIC ACID / AGAP001556-PA
Similarity search - Component
Biological speciesAnopheles gambiae (African malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLagarde, A. / Spinelli, S. / Tegoni, M. / Field, L. / He, X. / Zhou, J.J. / Cambillau, C.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: The Crystal Structure of Odorant Binding Protein 7 from Anopheles gambiae Exhibits an Outstanding Adaptability of Its Binding Site.
Authors: Lagarde, A. / Spinelli, S. / Tegoni, M. / He, X. / Field, L. / Zhou, J.J. / Cambillau, C.
History
DepositionMar 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2011Group: Database references
Revision 1.2Dec 21, 2011Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Odorant binding protein, antennal
B: Odorant binding protein, antennal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2564
Polymers28,7432
Non-polymers5132
Water3,441191
1
A: Odorant binding protein, antennal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6282
Polymers14,3721
Non-polymers2561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Odorant binding protein, antennal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6282
Polymers14,3721
Non-polymers2561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.704, 46.469, 57.438
Angle α, β, γ (deg.)90.00, 103.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Odorant binding protein, antennal / OBP 7 / Odorant-binding protein AgamOBP7


Mass: 14371.638 Da / Num. of mol.: 2 / Fragment: UNP residues 29-154
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles gambiae (African malaria mosquito)
Gene: OBP7, AgamOBP7, AGAP001556, agCG57323 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7PXT9
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.11 Å3/Da / Density % sol: 41.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.75
Details: 33 mM HEPES, pH 7.25-8.25, 0.4-1.0 M KCl, 6.6 mM sodium borate, 0.83 M sodium citrate tribasic, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 1, 2010
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.1→55.8 Å / Num. all: 14055 / Num. obs: 14055 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 20.34 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 22.1
Reflection shellResolution: 2.1→2.2 Å / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 8.8 / % possible all: 99.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
BUSTER2.9.2refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ERB

2erb


Resolution: 2.1→55.79 Å / Cor.coef. Fo:Fc: 0.8506 / Cor.coef. Fo:Fc free: 0.8403 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT/BUSTER
RfactorNum. reflection% reflectionSelection details
Rfree0.289 995 7.19 %RANDOM
Rwork0.2723 ---
obs0.2735 13831 --
all-13831 --
Displacement parametersBiso mean: 21.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.4426 Å20 Å23.2827 Å2
2--1.7811 Å20 Å2
3----1.3385 Å2
Refine analyzeLuzzati coordinate error obs: 0.437 Å
Refinement stepCycle: LAST / Resolution: 2.1→55.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1751 0 36 191 1978
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0091823HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.252463HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d22619SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes343HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3254HARMONIC5
X-RAY DIFFRACTIONt_it01823HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.99
X-RAY DIFFRACTIONt_other_torsion21.87
X-RAY DIFFRACTIONt_chiral_improper_torsion0251SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact02294SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.27 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.4289 201 7.36 %
Rwork0.4252 2529 -
all0.4254 2730 -
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)
10.0905-0.03280.1570.140.16430.40260.001-0.00590.00370.00020.0035-0.0035-0.00110.001-0.00440.01430.0087-0.01630.00820.0097-0.01534.9494-0.08074.8904
20.1974-0.0232-0.03280.0417-0.03280.09480.0007-0.00060.0036-0.0021-0.0003-0.0017-0.0020.0013-0.00040.00430.0066-0.00780.00950.001-0.001911.18312.7701-0.7827
30.1055-0.13870.01660.1370.10610.37470-0.00190.0022-0.0006-0.00140.00130.00240.00120.00140.01110.0051-0.00450.00330.0028-0.0058-1.5823-20.724133.9184
40.09820.0378-0.00210.1199-0.08780.1219-0.0015-0.0010.0061-0.00450.0023-0.00250.00030.0004-0.00080.01050.001-0.01180.00790.0046-0.00875.2174-18.328.4486
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|15 - A|82}A15 - 82
2X-RAY DIFFRACTION2{A|92 - A|133}A92 - 133
3X-RAY DIFFRACTION3{B|11 - B|82}B11 - 82
4X-RAY DIFFRACTION4{B|92 - B|133}B92 - 133

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