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- PDB-7tx8: Long form D7 protein from Anopheles darlingi with U46619 and sero... -

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Basic information

Entry
Database: PDB / ID: 7tx8
TitleLong form D7 protein from Anopheles darlingi with U46619 and serotonin bound
ComponentsLong form D7 salivary protein
KeywordsBLOOD CLOTTING / odorant-binding
Function / homologyPheromone/general odorant binding protein superfamily / odorant binding / sensory perception of smell / toxin activity / extracellular space / Chem-PUC / SEROTONIN / Long form salivary protein D7L2
Function and homology information
Biological speciesAnopheles darlingi (American malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.51 Å
AuthorsAndersen, J.F. / Alvarenga, P.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Insect Biochem.Mol.Biol. / Year: 2022
Title: Functional aspects of evolution in a cluster of salivary protein genes from mosquitoes.
Authors: Alvarenga, P.H. / Dias, D.R. / Xu, X. / Francischetti, I.M.B. / Gittis, A.G. / Arp, G. / Garboczi, D.N. / Ribeiro, J.M.C. / Andersen, J.F.
History
DepositionFeb 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Long form D7 salivary protein
B: Long form D7 salivary protein
C: Long form D7 salivary protein
D: Long form D7 salivary protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,67512
Polymers139,5684
Non-polymers2,1078
Water2,846158
1
A: Long form D7 salivary protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4193
Polymers34,8921
Non-polymers5272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Long form D7 salivary protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4193
Polymers34,8921
Non-polymers5272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Long form D7 salivary protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4193
Polymers34,8921
Non-polymers5272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Long form D7 salivary protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4193
Polymers34,8921
Non-polymers5272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.060, 98.060, 273.930
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
Long form D7 salivary protein


Mass: 34892.090 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles darlingi (American malaria mosquito)
Production host: Escherichia coli (E. coli) / References: UniProt: B6DDQ8
#2: Chemical
ChemComp-SRO / SEROTONIN / 3-(2-AMINOETHYL)-1H-INDOL-5-OL


Mass: 176.215 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H12N2O / Comment: neurotransmitter*YM
#3: Chemical
ChemComp-PUC / (5Z)-7-{(1R,4S,5S,6R)-6-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-2-oxabicyclo[2.2.1]hept-5-yl}hept-5-enoic acid / 15-Hydroxy-11 alpha,9 alpha-(epoxymethano)prosta-5,13-dienoic Acid


Mass: 350.492 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H34O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.72 Å3/Da / Density % sol: 54.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M ammonium sulfate, 30% PEG 5000 MME, 0.1 M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.51→53.31 Å / Num. obs: 53228 / % possible obs: 100 % / Redundancy: 22.06 % / Biso Wilson estimate: 59.01 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.086 / Χ2: 0.933 / Net I/σ(I): 25.46 / Num. measured all: 1174205 / Scaling rejects: 103
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.51-2.5823.120.6396.1289915388938890.9620.653100
2.58-2.6523.0010.5357.2387241379337930.9740.547100
2.65-2.7222.6090.4228.8882590365336530.9840.432100
2.72-2.8121.970.35410.1778543357535750.9870.362100
2.81-2.920.0760.26312.4469483346134610.9920.27100
2.9-323.450.22116.1478839336233620.9950.225100
3-3.1123.6650.1819.0576226322132210.9960.184100
3.11-3.2423.4630.14323.8174285316631660.9970.146100
3.24-3.3823.0610.11728.669438301130110.9980.12100
3.38-3.5522.6120.09932.6565124288028800.9980.102100
3.55-3.7422.2020.08835.7360524272627260.9980.09100
3.74-3.9721.3330.0838.9255615260726070.9990.081100
3.97-4.2418.830.07239.7146622247624760.9990.074100
4.24-4.5821.8730.06944.949390225922580.9990.07100
4.58-5.0222.2350.06746.3647849215221520.9990.069100
5.02-5.6121.8830.06646.1842059192219220.9990.067100
5.61-6.4821.1820.06446.1636751173517350.9990.065100
6.48-7.9419.2790.0645.228147146014600.9990.061100
7.94-11.2319.3010.05747.522833118311830.9990.059100
11.23-53.3118.2390.05645.59127317016980.9990.05899.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.51 Å84.92 Å
Translation2.51 Å84.92 Å

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: unliganded AnDar-D7L2

Resolution: 2.51→53.31 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 2.35 / Phase error: 27.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2661 2556 4.87 %
Rwork0.2179 49937 -
obs0.2202 52493 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.89 Å2 / Biso mean: 62.1989 Å2 / Biso min: 33.25 Å2
Refinement stepCycle: final / Resolution: 2.51→53.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9407 0 308 158 9873
Biso mean--58.82 54.92 -
Num. residues----1176
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.51-2.560.36191250.3012610273595
2.56-2.610.351420.29792629277195
2.61-2.670.31821390.28392673281296
2.67-2.730.34361590.2772697285697
2.73-2.80.32321570.27182702285997
2.8-2.870.31751770.25842684286199
2.87-2.960.28931430.25592714285798
2.96-3.050.36231260.2622773289999
3.05-3.160.30451320.2672806293899
3.16-3.290.32731310.283227722903100
3.29-3.440.28861150.22327942909100
3.44-3.620.28081520.210928172969100
3.62-3.850.24541310.199127832914100
3.85-4.140.22891500.191628402990100
4.14-4.560.22211330.173328452978100
4.56-5.220.22681480.18628533001100
5.22-6.570.24251430.218329093052100
6.57-53.310.251530.20430363189100
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)
11.315-0.1033-0.82511.55120.69113.81580.17270.0726-0.201-0.068-0.24290.23260.1416-0.22530.0610.26840.0378-0.03810.3653-0.0720.477412.545429.0476-37.8699
21.4196-0.5586-0.13851.3043-1.78384.0789-0.24760.13510.15810.3708-0.075-0.321-0.33470.29070.28730.6038-0.0972-0.13680.38610.02850.5533-31.28360.5553-9.4409
32.26670.1581-0.77921.9448-1.50494.10280.0529-0.0149-0.3095-0.2323-0.1949-0.03070.4079-0.11010.15330.2832-0.0268-0.00110.3494-0.05050.4777-18.411628.0469-58.1677
41.21850.1499-2.11972.0237-0.29454.6846-0.1620.015-0.20380.30610.0067-0.20090.05210.30790.15830.4239-0.1365-0.01960.54750.04920.5233-17.496628.289411.2742
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 3 through 297)A3 - 297
2X-RAY DIFFRACTION2(chain 'B' and resid 3 through 297)B3 - 297
3X-RAY DIFFRACTION3(chain 'C' and resid 3 through 297)C3 - 297
4X-RAY DIFFRACTION4(chain 'D' and resid 3 through 297)D3 - 297

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