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- PDB-6xl7: Structure of a mosquito complement inhibitor from Anopheles freeborni -

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Basic information

Entry
Database: PDB / ID: 6xl7
TitleStructure of a mosquito complement inhibitor from Anopheles freeborni
ComponentsSG7.AF
KeywordsPROTEIN BINDING / Inhibitor / complement / alternative pathway / C3bBb
Biological speciesAnopheles freeborni (western malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.42 Å
AuthorsAndersen, J.F. / Strayer, E.
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 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 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 1.2Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 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

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Assembly

Deposited unit
A: SG7.AF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2646
Polymers13,8441
Non-polymers4205
Water3,999222
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.980, 85.980, 46.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-310-

HOH

21A-315-

HOH

31A-511-

HOH

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Components

#1: Protein SG7.AF


Mass: 13843.864 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles freeborni (western malaria mosquito)
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 222 / 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: 3.08 Å3/Da / Density % sol: 60.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.8 M ammonium sulfate, 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.42→31.43 Å / Num. obs: 32895 / % possible obs: 99.2 % / Redundancy: 12.925 % / Biso Wilson estimate: 21.644 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.054 / Χ2: 1.044 / Net I/σ(I): 31.38 / Num. measured all: 425154 / Scaling rejects: 102
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
1.42-1.464.5010.2225.349655242121450.9520.2588.6
1.46-1.511.3750.19510.8926776235523540.990.204100
1.5-1.5413.6050.16114.6331088228522850.9940.167100
1.54-1.5913.5570.13717.0130002221322130.9950.142100
1.59-1.6413.4870.11420.4429212216621660.9960.119100
1.64-1.713.40.09823.227845207820780.9970.102100
1.7-1.7613.6590.08925.6127632202320230.9980.093100
1.76-1.8314.0070.07929.6827384195519550.9980.082100
1.83-1.9114.1780.06933.8126768188818880.9990.071100
1.91-2.0114.1230.0638.8125153178117810.9990.063100
2.01-2.1214.0380.05542.0923935170517050.9990.057100
2.12-2.2513.9560.0545.9222609162016200.9990.052100
2.25-2.413.8610.04747.9321207153015300.9990.048100
2.4-2.5913.8460.04649.2819869143514350.9990.048100
2.59-2.8413.8640.04350.3518231131513150.9990.044100
2.84-3.1813.7240.04352.2316757122112210.9990.044100
3.18-3.6713.5410.04153.9314462106810680.9980.043100
3.67-4.4913.2390.04754.51124059379370.9990.049100
4.49-6.3512.8320.04852.8694197347340.9980.05100
6.35-31.4310.7350.05848.0647454434420.9970.06299.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å40.61 Å
Translation3 Å40.61 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASER2.7.17phasing
PHENIX1.18.2refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: albicin

Resolution: 1.42→31.43 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.51 / Phase error: 17.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1932 1598 4.89 %
Rwork0.1792 31065 -
obs0.1798 32663 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.27 Å2 / Biso mean: 20.3324 Å2 / Biso min: 6.24 Å2
Refinement stepCycle: final / Resolution: 1.42→31.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms970 0 21 222 1213
Biso mean--39.68 31.54 -
Num. residues----119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051052
X-RAY DIFFRACTIONf_angle_d0.8551427
X-RAY DIFFRACTIONf_dihedral_angle_d26.267407
X-RAY DIFFRACTIONf_chiral_restr0.077157
X-RAY DIFFRACTIONf_plane_restr0.005178
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.42-1.470.23751430.21782433257687
1.47-1.520.19451410.18722762290398
1.52-1.580.19331480.17962804295299
1.58-1.650.21021480.17992809295799
1.65-1.740.22251320.180328252957100
1.74-1.850.21791450.189928352980100
1.85-1.990.20361630.178728352998100
1.99-2.190.20041440.169728593003100
2.19-2.510.17661560.16428833039100
2.51-3.160.16751340.183929323066100
3.16-31.430.19351440.180430883232100
Refinement TLS params.Method: refined / Origin x: 27.3719 Å / Origin y: 0.9709 Å / Origin z: 53.6677 Å
111213212223313233
T0.0865 Å20.0121 Å2-0.0022 Å2-0.0791 Å20.0051 Å2--0.0678 Å2
L0.4778 °20.4736 °2-0.0843 °2-4.7739 °20.6918 °2--0.6024 °2
S-0.0176 Å °-0.0223 Å °-0.041 Å °0.1196 Å °0.0425 Å °-0.1155 Å °0.0502 Å °-0.0147 Å °-0.0174 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 1 through 119)

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