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- PDB-6xmb: Structure of an anophensin from Anopheles stephensi -

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Basic information

Entry
Database: PDB / ID: 6xmb
TitleStructure of an anophensin from Anopheles stephensi
ComponentsAnophensin
KeywordsPROTEIN BINDING / Inhibitor / complement / alternative pathway / C3bBb / contact pathway
Function / homologytoxin activity / extracellular region / gSG7 salivary protein
Function and homology information
Biological speciesAnopheles stephensi (Asian malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.31 Å
AuthorsAndersen, J.F. / Strayer, E. / Lu, S.
Citation
Journal: J.Biol.Chem. / Year: 2020
Title: Salivary complement inhibitors from mosquitoes: Structure and mechanism of action.
Authors: Strayer, E.C. / Lu, S. / Ribeiro, J. / Andersen, J.F.
#1: Journal: J. Immunol. / Year: 2016
Title: An Inhibitor of the Alternative Pathway of Complement in Saliva of New World Anopheline Mosquitoes.
Authors: Mendes-Sousa, A.F. / Queiroz, D.C. / Vale, V.F. / Ribeiro, J.M. / Valenzuela, J.G. / Gontijo, N.F. / Andersen, J.F.
History
DepositionJun 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine / struct
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_method_to_determine_struct / _refine.pdbx_starting_model / _struct.title
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anophensin
B: Anophensin
C: Anophensin


Theoretical massNumber of molelcules
Total (without water)41,6373
Polymers41,6373
Non-polymers00
Water00
1
A: Anophensin
B: Anophensin


Theoretical massNumber of molelcules
Total (without water)27,7582
Polymers27,7582
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-34 kcal/mol
Surface area13100 Å2
MethodPISA
2
C: Anophensin

C: Anophensin


Theoretical massNumber of molelcules
Total (without water)27,7582
Polymers27,7582
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3400 Å2
ΔGint-36 kcal/mol
Surface area12510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.280, 82.360, 71.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Anophensin


Mass: 13878.906 Da / Num. of mol.: 3 / Fragment: UNP residues 23-142
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles stephensi (Asian malaria mosquito)
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: A5HUP6
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: 2.4 Å3/Da / Density % sol: 48.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 7% PEG10000, 0.1 M Tris-HCl

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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: Oct 20, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.31→35.71 Å / Num. obs: 18055 / % possible obs: 100 % / Redundancy: 7.886 % / Biso Wilson estimate: 60.396 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.063 / Χ2: 1.033 / Net I/σ(I): 19.44 / Num. measured all: 142373 / Scaling rejects: 10
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
2.31-2.377.8680.5774.1210299130913090.9510.618100
2.37-2.447.8050.5064.659866126412640.9590.542100
2.44-2.517.8140.3965.539767125012500.9810.425100
2.51-2.587.8120.2977.229546122212220.9840.318100
2.58-2.677.790.2588.069208118211820.9890.277100
2.67-2.767.9090.18410.598771110911090.9940.197100
2.76-2.878.090.15212.568948110611060.9940.163100
2.87-2.988.1720.11215.748703106510650.9970.119100
2.98-3.118.1740.117.848280101310130.9980.107100
3.11-3.278.1550.07921.479279739720.9980.08599.9
3.27-3.448.1280.06326.9176249389380.9980.067100
3.44-3.658.0820.05331.3470888778770.9980.056100
3.65-3.97.9440.04734.3166578388380.9980.051100
3.9-4.227.9170.04636.762317877870.9980.049100
4.22-4.627.8650.0439.5556477187180.9980.043100
4.62-5.177.7530.04139.4751876696690.9990.044100
5.17-5.967.7010.0438.8744825825820.9990.043100
5.96-7.317.4350.04339.0937405035030.9970.046100
7.31-10.337.2410.03941.0229474074070.9980.042100
10.33-35.715.9630.05636.8314552482440.9950.06298.4

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.31→35.71 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.49 / Phase error: 33.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2587 901 5.26 %
Rwork0.2287 16241 -
obs0.2305 17142 94.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.59 Å2 / Biso mean: 61.8948 Å2 / Biso min: 30.29 Å2
Refinement stepCycle: final / Resolution: 2.31→35.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2727 0 0 0 2727
Num. residues----349
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.31-2.450.32441370.27442407254487
2.45-2.640.30671250.28072561268691
2.64-2.910.39931280.29392708283695
2.91-3.330.32721400.28232778291898
3.33-4.20.27521740.22682832300699
4.2-35.710.20321970.18792955315299
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)
11.3014-0.0610.08810.0014-0.06230.23430.4667-0.2365-0.55760.3124-0.239-0.23260.23510.00130.00090.3638-0.006-0.05090.32620.03380.37482.31816.5003-27.0009
21.06070.16540.05461.5082-1.41792.2352-0.34730.18970.8217-0.4769-0.13730.4494-0.3965-0.0098-0.00030.49870.0194-0.11990.38720.00720.49938.362619.3865-29.9643
30.52780.51890.0320.7813-0.26351.15350.3951-0.3676-0.83320.3932-0.0081-0.16370.1045-0.13120.01410.37730.0678-0.03610.3822-0.02830.4475-6.79236.7578-22.7347
41.3201-0.03890.10552.12440.64550.5042-0.54620.04190.779-0.15040.25170.7134-0.36080.0419-0.00270.4390.0564-0.03460.4483-0.07760.5797-16.483212.8773-30.0177
50.06360.15770.08661.51430.65570.2830.23170.67070.31150.0372-0.26620.10610.0490.0280.00980.4154-0.04040.01120.59210.10290.5413-4.9896-3.1826-11.7858
60.6664-0.07170.75770.652-0.64041.3875-0.4232-0.9613-0.21351.1890.31020.43030.2414-0.169-0.00480.83220.03060.19060.7606-0.03890.5342-11.9227-3.9599-1.2409
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 58 )A2 - 58
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 119 )A59 - 119
3X-RAY DIFFRACTION3chain 'B' and (resid 3 through 58 )B3 - 58
4X-RAY DIFFRACTION4chain 'B' and (resid 59 through 120 )B59 - 120
5X-RAY DIFFRACTION5chain 'C' and (resid 5 through 58 )C5 - 58
6X-RAY DIFFRACTION6chain 'C' and (resid 59 through 118 )C59 - 118

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