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- PDB-3k1e: Crystal structure of odorant binding protein 1 (AaegOBP1) from Ae... -

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Basic information

Entry
Database: PDB / ID: 3k1e
TitleCrystal structure of odorant binding protein 1 (AaegOBP1) from Aedes aegypti
ComponentsOdorant binding proteinOdorant-binding protein
KeywordsODORANT BINDING PROTEIN / Insect odorant binding protein fold
Function / homology
Function and homology information


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
Biological speciesAedes aegypti (yellow fever mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLeite, N.R. / Krogh, R. / Leal, W.S. / Iulek, J. / Oliva, G.
CitationJournal: Plos One / Year: 2009
Title: Structure of an odorant-binding protein from the mosquito Aedes aegypti suggests a binding pocket covered by a pH-sensitive "Lid".
Authors: Leite, N.R. / Krogh, R. / Xu, W. / Ishida, Y. / Iulek, J. / Leal, W.S. / Oliva, G.
History
DepositionSep 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Sep 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 / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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)30,5937
Polymers29,2642
Non-polymers1,3305
Water7,386410
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.248, 47.870, 69.082
Angle α, β, γ (deg.)90.00, 96.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 14631.783 Da / Num. of mol.: 2 / Fragment: UNP residues 19-143
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Gene: AAEL009449 / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6Y2R8
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: 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.: 1 / Source method: obtained synthetically / Formula: C55H112O28 / Comment: precipitant*YM
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 1.92 Å3/Da / Density % sol: 36.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2 microliter drops, with equal volumes of protein at 50 mg/mL and reservoir solution containing 28% PEG 8000, 250 mM MgCl2, 50 mM Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 27, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.85→70 Å / Num. all: 19077 / Num. obs: 19077 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 21.43 Å2 / Rsym value: 0.071 / Net I/σ(I): 20.35
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 7.38 % / Mean I/σ(I) obs: 4.4 / Rsym value: 0.547 / % possible all: 98.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0072refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2ERB

2erb


Resolution: 1.85→68.68 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.619 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.212 972 5.1 %RANDOM
Rwork0.151 ---
obs0.154 19077 99.6 %-
all-19077 --
Solvent computationIon probe radii: 0.4 Å / Shrinkage radii: 0.5 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.91 Å2
Baniso -1Baniso -2Baniso -3
1--1.34 Å20 Å2-0.11 Å2
2--1.22 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.85→68.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1935 0 59 410 2404
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222218
X-RAY DIFFRACTIONr_bond_other_d0.0010.021556
X-RAY DIFFRACTIONr_angle_refined_deg1.1882.0043027
X-RAY DIFFRACTIONr_angle_other_deg0.8243.0073724
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8745285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67824.712104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.61815392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.398156
X-RAY DIFFRACTIONr_chiral_restr0.0680.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212407
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02415
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.73321277
X-RAY DIFFRACTIONr_mcbond_other0.2072497
X-RAY DIFFRACTIONr_mcangle_it1.22232093
X-RAY DIFFRACTIONr_scbond_it2.1374.5941
X-RAY DIFFRACTIONr_scangle_it3.1146910
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 73 -
Rwork0.229 1343 -
obs--98.68 %
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)
14.3531-0.8885-0.8442.8764-0.26163.6997-0.0016-0.25910.17190.2440.019-0.0751-0.14670.0711-0.01730.0254-0.0034-0.0040.0159-0.00970.00748.208141.554621.9613
24.7879-0.42530.10713.11461.03042.5075-0.0322-0.2156-0.11060.15980.0086-0.07450.11020.05170.02360.00980.0025-0.00210.01140.00680.006326.626819.371510.9283
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 125
2X-RAY DIFFRACTION1A126 - 201
3X-RAY DIFFRACTION1A203 - 489
4X-RAY DIFFRACTION2B10 - 125
5X-RAY DIFFRACTION2B126 - 202
6X-RAY DIFFRACTION2B203 - 509

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