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- PDB-7fit: Crystal structure of Wolbachia cytoplasmic incompatibility factor... -

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Basic information

Entry
Database: PDB / ID: 7fit
TitleCrystal structure of Wolbachia cytoplasmic incompatibility factor CidA from wMel
Componentsbacteria factor 1
KeywordsANTITOXIN / Wolbachia / cytoplasmic incompatibility
Function / homologyCytoplasmic incompatibility factor CifA
Function and homology information
Biological speciesWolbachia endosymbiont of Drosophila melanogaster (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.75 Å
AuthorsXiao, Y.J. / Wang, W. / Chen, X. / Ji, X.Y. / Yang, H.T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81772204 China
CitationJournal: Nat Commun / Year: 2022
Title: Crystal Structures of Wolbachia CidA and CidB Reveal Determinants of Bacteria-induced Cytoplasmic Incompatibility and Rescue.
Authors: Wang, H. / Xiao, Y. / Chen, X. / Zhang, M. / Sun, G. / Wang, F. / Wang, L. / Zhang, H. / Zhang, X. / Yang, X. / Li, W. / Wei, Y. / Yao, D. / Zhang, B. / Li, J. / Cui, W. / Wang, F. / Chen, C. ...Authors: Wang, H. / Xiao, Y. / Chen, X. / Zhang, M. / Sun, G. / Wang, F. / Wang, L. / Zhang, H. / Zhang, X. / Yang, X. / Li, W. / Wei, Y. / Yao, D. / Zhang, B. / Li, J. / Cui, W. / Wang, F. / Chen, C. / Shen, W. / Su, D. / Bai, F. / Huang, J. / Ye, S. / Zhang, L. / Ji, X. / Wang, W. / Wang, Z. / Hochstrasser, M. / Yang, H.
History
DepositionAug 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: bacteria factor 1


Theoretical massNumber of molelcules
Total (without water)55,6421
Polymers55,6421
Non-polymers00
Water52229
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)109.882, 109.882, 79.087
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein bacteria factor 1


Mass: 55642.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wolbachia endosymbiont of Drosophila melanogaster (bacteria)
Gene: WD_0631 / Production host: Escherichia coli (E. coli) / References: UniProt: Q73HD5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

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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: 2.53 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 289.15 K / Method: batch mode
Details: 0.2M Sodium phosphate monobasic monohydrate, 20% w/v Polyethylene glycol 3350, pH 4.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 14273 / % possible obs: 99.9 % / Redundancy: 17.4 % / Biso Wilson estimate: 68.52 Å2 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.041 / Rrim(I) all: 0.17 / Χ2: 2.05 / Net I/σ(I): 5.6 / Num. measured all: 249034
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.75-2.818.51.6036920.8460.3831.6490.633100
2.8-2.8518.31.137210.8890.2711.1620.62699.9
2.85-2.918.31.0587060.910.2551.0880.654100
2.9-2.96180.8667110.9390.210.8910.7399.9
2.96-3.0317.90.7267000.9410.1770.7480.841100
3.03-3.116.80.6436960.9510.1620.6630.94599.7
3.1-3.1716.70.5677230.9590.1430.5851.12100
3.17-3.2619.40.5157120.9750.120.5291.186100
3.26-3.3619.30.4827070.9760.1120.4951.416100
3.36-3.4615.80.4637140.9730.120.4792.403100
3.46-3.5917.90.4077180.9840.0990.4192.452100
3.59-3.73170.2766980.9840.0690.2852.807100
3.73-3.9160.2457130.9890.0640.2543.051100
3.9-4.11150.2037240.9920.0550.2112.993100
4.11-4.3618.10.1597180.9950.0390.1642.962100
4.36-4.718.50.1317100.9930.0320.1343.195100
4.7-5.17180.127170.9910.0290.1233.192100
5.17-5.9217.10.127240.9970.030.1243.076100
5.92-7.4617.30.1027270.9980.0250.1053.434100
7.46-5015.30.0677420.9990.0180.0693.89199.1

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.75→32.74 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2543 1426 10.04 %
Rwork0.1985 12772 -
obs0.2039 14198 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 218.83 Å2 / Biso mean: 92.2452 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.75→32.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2850 0 0 30 2880
Biso mean---68.38 -
Num. residues----360
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.75-2.850.33351400.24441263140399
2.85-2.960.27581420.236512681410100
2.96-3.090.32811440.235612641408100
3.09-3.260.30161390.229812881427100
3.26-3.460.27661400.2341267140799
3.46-3.730.31281430.22191257140099
3.73-4.10.24981360.20241282141898
4.1-4.690.22041500.173612741424100
4.7-5.90.24971420.196612981440100
5.91-32.740.22051500.17181311146199
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)
12.15642.6911-0.42995.44942.34258.389-0.54-0.83840.136-0.4736-0.39540.6984-1.5788-0.65630.76590.79590.2721-0.39551.2803-0.08921.1349-18.11133.519510.9036
25.40811.0854-0.44716.09130.88836.7371-0.7017-1.9242-0.051.74650.8599-0.6075-0.3121.5642-0.22091.39920.3537-0.44911.78640.13831.7617-8.813428.619613.4408
34.9693-0.57242.12592.3913-0.674.2855-0.20790.3242-0.54890.3313-0.1245-1.45120.01350.67290.32680.68350.1234-0.19971.04020.13731.5869-3.125527.98064.3929
44.6964-1.15482.33714.7801-0.61977.14510.21110.0516-0.8523-0.1815-0.1449-0.55160.84760.66090.01890.62490.13040.13240.74220.04081.1836-11.579226.0764-11.0601
58.9841-1.0761-2.53044.43570.17928.8926-0.16560.73040.3639-0.4865-0.0344-0.2430.3265-0.00330.20540.38370.04030.08420.33910.06470.5418-25.978234.6496-15.239
64.5833-0.8371-2.62574.93623.35865.1206-0.29971.10030.8777-0.97770.0167-0.6859-0.9069-0.15270.05520.5771-0.1210.14290.67690.15350.6134-28.776144.052-15.5389
78.1898-1.6751-0.9614.3958-0.65555.96250.15820.51740.4594-0.1532-0.192-0.3974-0.16190.43730.10090.3421-0.05660.0220.44870.0140.4509-36.960442.4508-5.8658
88.3671-0.11082.32815.2675-0.97347.0242-0.1798-0.76380.47280.62980.00090.0291-0.2463-0.20130.11480.4333-0.05230.02530.4312-0.08490.3262-47.419145.71864.2571
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 40 )A5 - 40
2X-RAY DIFFRACTION2chain 'A' and (resid 41 through 65 )A41 - 65
3X-RAY DIFFRACTION3chain 'A' and (resid 66 through 107 )A66 - 107
4X-RAY DIFFRACTION4chain 'A' and (resid 108 through 228 )A108 - 228
5X-RAY DIFFRACTION5chain 'A' and (resid 229 through 258 )A229 - 258
6X-RAY DIFFRACTION6chain 'A' and (resid 259 through 286 )A259 - 286
7X-RAY DIFFRACTION7chain 'A' and (resid 287 through 332 )A287 - 332
8X-RAY DIFFRACTION8chain 'A' and (resid 333 through 422 )A333 - 422

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