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- PDB-6xke: Structure of a mosquito complement inhibitor from Anopheles albimanus -

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Basic information

Entry
Database: PDB / ID: 6xke
TitleStructure of a mosquito complement inhibitor from Anopheles albimanus
ComponentsAlbicin
KeywordsPROTEIN BINDING / Inhibitor / complement / alternative pathway / C3bBb
Function / homologyBROMIDE ION / Secreted protein
Function and homology information
Biological speciesAnopheles albimanus (mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 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 26, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Albicin
B: Albicin
C: Albicin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,02311
Polymers40,3843
Non-polymers6398
Water7,494416
1
A: Albicin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6213
Polymers13,4611
Non-polymers1602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Albicin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7815
Polymers13,4611
Non-polymers3204
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Albicin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6213
Polymers13,4611
Non-polymers1602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.680, 137.680, 61.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-202-

BR

21C-396-

HOH

31C-428-

HOH

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Components

#1: Protein Albicin


Mass: 13461.331 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles albimanus (mosquito) / Plasmid: pET17b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: A0A1Y9G8D0
#2: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.95 Å3/Da / Density % sol: 58.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20% PEG 3350, 0.2 M ammonium fluoride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9184 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 23, 2017
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.55→52.41 Å / Num. obs: 68450 / % possible obs: 98.2 % / Redundancy: 11.06 % / Biso Wilson estimate: 24.181 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.082 / Χ2: 1.047 / Net I/σ(I): 19.14 / Num. measured all: 757079 / Scaling rejects: 862
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
1.55-1.593.6290.4492.7713815507538070.8420.51475
1.59-1.648.4940.4314.9542437499849960.9350.459100
1.64-1.6911.7820.3527.4256493479547950.9730.369100
1.69-1.7411.6410.2988.6654843471147110.9790.312100
1.74-1.7911.6520.24310.3453028455145510.9850.255100
1.79-1.8611.5650.20112.2150944440544050.9880.211100
1.86-1.9311.5550.16214.6949142425542530.9910.17100
1.93-2.0111.770.13117.9348364411041090.9940.137100
2.01-2.111.8950.10521.447141396439630.9960.109100
2.1-2.211.9750.0932444895375037490.9960.097100
2.2-2.3211.9720.08426.4543052359935960.9970.08899.9
2.32-2.4611.9960.07727.8241076342734240.9970.08199.9
2.46-2.6312.0010.07229.9238222318931850.9970.07699.9
2.63-2.8411.9810.0731.0136219302430230.9980.073100
2.84-3.1111.9650.06532.8633011275927590.9980.068100
3.11-3.4811.8390.05834.4230058253925390.9990.061100
3.48-4.0111.7030.05735.4726309224822480.9980.06100
4.01-4.9211.6210.05735.7322196191019100.9980.059100
4.92-6.9511.1120.06433.9217002153015300.9980.067100
6.95-52.419.8460.07532.5288328998970.9950.07999.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
XDSNov 1, 2016data reduction
XSCALENov 1, 2016data scaling
SHELX2016/1phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.55→52.41 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.48 / Phase error: 18.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2031 3193 4.76 %
Rwork0.1826 63909 -
obs0.1836 67102 96.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.42 Å2 / Biso mean: 20.1213 Å2 / Biso min: 8.11 Å2
Refinement stepCycle: final / Resolution: 1.55→52.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2832 0 8 416 3256
Biso mean--35.59 26.36 -
Num. residues----348
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.580.2727750.24211512158753
1.58-1.60.22811470.20472542268990
1.6-1.630.21361300.18472680281094
1.63-1.660.21421380.17722709284795
1.66-1.690.19761400.17462733287397
1.69-1.720.22711360.18242787292397
1.72-1.750.23651260.1872787291397
1.75-1.790.23811230.18952833295698
1.79-1.830.20061220.18552830295298
1.83-1.880.22051490.17932807295699
1.88-1.930.1741580.18052813297199
1.93-1.990.18271410.17772864300599
1.99-2.050.18361170.17472841295899
2.05-2.130.19751510.172861301299
2.13-2.210.1941350.180828713006100
2.21-2.310.20471370.172728633000100
2.31-2.430.21161620.182728823044100
2.43-2.590.17371680.177228583026100
2.59-2.780.23911580.199628863044100
2.78-3.060.21781370.192929283065100
3.06-3.510.20881270.178629493076100
3.51-4.420.1981580.164529683126100
4.42-52.410.18491580.199931053263100
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)
10.8821-0.128-0.12532.2491-1.60224.26220.03360.0286-0.01160.08360.0193-0.02630.1038-0.0157-0.04870.08310.01390.00660.101-0.00460.107415.618211.558142.8573
21.0747-0.29490.19693.4157-1.0120.9635-0.0004-0.0181-0.02680.003-0.011-0.05030.02390.0420.0130.0346-0.00480.00670.10490.00020.074630.837831.113529.048
31.3737-0.6333-0.0653.33430.33911.46770.01840.05110.0448-0.2122-0.0075-0.09230.12710.0329-0.00210.14870.00440.00980.11950.00160.050123.843819.293112.2378
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 116)A1 - 116
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 116)B1 - 116
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 116)C1 - 116

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