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- PDB-3nhi: Crystal structure of the AnSt-D7L1-leukotriene C4 complex -

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Basic information

Entry
Database: PDB / ID: 3nhi
TitleCrystal structure of the AnSt-D7L1-leukotriene C4 complex
ComponentsD7 protein
KeywordsTRANSPORT PROTEIN / All helical / odorant-binding protein / ligand-binding protein / D7
Function / homology
Function and homology information


odorant binding / vasodilation / sensory perception of smell / toxin activity / extracellular space
Similarity search - Function
Pheromone/general odorant binding protein domain / 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
Chem-EAH / Long form salivary protein D7L1
Similarity search - Component
Biological speciesAnopheles stephensi (Asian malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.43 Å
AuthorsAndersen, J.F. / Alvarenga, P.H. / Francischetti, I.M. / Calvo, E. / Sa-Nunes, A. / Ribeiro, J.M.
CitationJournal: Plos Biol. / Year: 2010
Title: The function and three-dimensional structure of a thromboxane a(2)/cysteinyl leukotriene-binding protein from the saliva of a mosquito vector of the malaria parasite.
Authors: Alvarenga, P.H. / Francischetti, I.M. / Calvo, E. / Sa-Nunes, A. / Ribeiro, J.M. / Andersen, J.F.
History
DepositionJun 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: D7 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9614
Polymers34,4521
Non-polymers5093
Water9,134507
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.968, 40.906, 68.387
Angle α, β, γ (deg.)90.000, 110.680, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein D7 protein / Long form D7clu2 salivary protein


Mass: 34452.082 Da / Num. of mol.: 1 / Fragment: UNP residues 20-315
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles stephensi (Asian malaria mosquito)
Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3)pLysS / References: UniProt: Q95NY5
#2: Chemical ChemComp-EAH / (5S,7E,9E,11Z,14Z)-5-hydroxyicosa-7,9,11,14-tetraenoic acid


Mass: 320.466 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H32O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 507 / 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: 2.2 Å3/Da / Density % sol: 44.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30 % PEG 3000, 0.2 M Lithium sulfate, 0.1 M Tris HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 18, 2009
RadiationMonochromator: Double crystal Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.43→50 Å / Num. all: 55648 / Num. obs: 55648 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.043 / Χ2: 1.161 / Net I/σ(I): 16.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.43-1.453.50.30326771.04894.8
1.45-1.484.10.28427121.00998.8
1.48-1.514.50.2427551.08599
1.51-1.544.50.22127471.08399.2
1.54-1.574.60.18827611.1199.6
1.57-1.614.70.15927651.1399.9
1.61-1.654.70.14127601.133100
1.65-1.74.80.12628111.146100
1.7-1.754.80.11227391.151100
1.75-1.84.90.09827901.217100
1.8-1.874.90.08228091.22100
1.87-1.944.90.06827721.297100
1.94-2.034.90.05828011.352100
2.03-2.144.90.04528021.322100
2.14-2.2750.03827841.272100
2.27-2.4550.03427901.212100
2.45-2.6950.0328091.139100
2.69-3.084.90.02528341.067100
3.08-3.884.90.02128331100
3.88-504.70.02228971.1399.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 27.41 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å25.75 Å
Translation2.5 Å25.75 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.43→25.75 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.189 / WRfactor Rwork: 0.1656 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9027 / SU B: 1.973 / SU ML: 0.036 / SU R Cruickshank DPI: 0.0657 / SU Rfree: 0.0658 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1902 2820 5.1 %RANDOM
Rwork0.1669 ---
obs0.1681 55636 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 86.19 Å2 / Biso mean: 13.3111 Å2 / Biso min: 3.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å2-0.1 Å2
2---0.25 Å20 Å2
3---0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.43→25.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2416 0 34 507 2957
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222544
X-RAY DIFFRACTIONr_angle_refined_deg1.1081.963437
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5315305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.91724.109129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.86515452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.611516
X-RAY DIFFRACTIONr_chiral_restr0.0790.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211945
X-RAY DIFFRACTIONr_mcbond_it0.5821.51489
X-RAY DIFFRACTIONr_mcangle_it1.1122396
X-RAY DIFFRACTIONr_scbond_it1.79331055
X-RAY DIFFRACTIONr_scangle_it2.984.51035
LS refinement shellResolution: 1.43→1.466 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.214 182 -
Rwork0.212 3736 -
all-3918 -
obs--96.01 %
Refinement TLS params.Method: refined / Origin x: 5.5021 Å / Origin y: 1.0883 Å / Origin z: 14.2145 Å
111213212223313233
T0.0116 Å20.0034 Å20.0015 Å2-0.0112 Å20.0027 Å2--0.0011 Å2
L0.3348 °20.0703 °20.0818 °2-0.1926 °2-0.0218 °2--0.0286 °2
S-0.0047 Å °-0.0182 Å °-0.0013 Å °0.0078 Å °0.0046 Å °-0.0008 Å °-0.0026 Å °-0.0053 Å °0.0002 Å °

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