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- PDB-3ngv: Crystal structure of AnSt-D7L1 -

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Basic information

Entry
Database: PDB / ID: 3ngv
TitleCrystal structure of AnSt-D7L1
ComponentsD7 protein
KeywordsTRANSPORT PROTEIN / All-helical / odorant-binding protein / D7 / Ligand binding protein
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
Long form salivary protein D7L1
Similarity search - Component
Biological speciesAnopheles stephensi (Asian malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsAndersen, J.F. / Alvarenga, P.H. / Francischetti, I.M. / Ribeiro, J.M. / Calvo, E.
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 13, 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: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Oct 9, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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)34,7364
Polymers34,4521
Non-polymers2843
Water7,116395
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.445, 56.664, 113.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 34452.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles stephensi (Asian malaria mosquito)
Gene: EUBVEN_02512 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q95NY5, EC: 5.99.1.2
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.36 Å3/Da / Density % sol: 47.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG 3000, 0.2M Lithium sulfate, 0.1M 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: 22-BM / Wavelength: 0.97242 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 6, 2009 / Details: Rosenbaum-Rock double crystal monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. all: 33020 / Num. obs: 33020 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Rmerge(I) obs: 0.053 / Χ2: 1.528 / Net I/σ(I): 32.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.76-1.8310.10.131541.58896.8
1.83-1.9110.50.08532881.685100
1.91-1.9910.50.07532271.538100
1.99-2.110.40.06732801.637100
2.1-2.2310.20.06132861.652100
2.23-2.410.10.05732931.627100
2.4-2.64100.05433101.625100
2.64-3.039.90.05133171.546100
3.03-3.819.50.0533791.15899.9
3.81-509.20.04434861.17798.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0 / SU B: 3.974 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2038 1666 5.1 %RANDOM
Rwork0.158 ---
all0.1603 33020 --
obs0.1603 32965 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 61.82 Å2 / Biso mean: 15.9185 Å2 / Biso min: 3.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.76→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2424 0 16 395 2835
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0222503
X-RAY DIFFRACTIONr_angle_refined_deg2.0511.9533382
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3915297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.56823.968126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35715445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9911516
X-RAY DIFFRACTIONr_chiral_restr0.1620.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211905
X-RAY DIFFRACTIONr_mcbond_it1.3621.51479
X-RAY DIFFRACTIONr_mcangle_it2.322375
X-RAY DIFFRACTIONr_scbond_it3.50831024
X-RAY DIFFRACTIONr_scangle_it5.6674.51006
LS refinement shellResolution: 1.76→1.807 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 115 -
Rwork0.186 2236 -
all-2351 -
obs-2351 96.08 %
Refinement TLS params.Method: refined / Origin x: -24.6818 Å / Origin y: -2.8351 Å / Origin z: 6.5989 Å
111213212223313233
T0.018 Å20.0032 Å20.01 Å2-0.0179 Å20.0005 Å2--0.0162 Å2
L0.1359 °20.0037 °2-0.1366 °2-0.1742 °20.0314 °2--0.3028 °2
S0.0492 Å °0.008 Å °0.0217 Å °-0.0036 Å °-0.0366 Å °-0.0077 Å °-0.0262 Å °-0.0322 Å °-0.0126 Å °

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