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- PDB-7fiw: Crystal structure of the complex formed by Wolbachia cytoplasmic ... -

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Basic information

Entry
Database: PDB / ID: 7fiw
TitleCrystal structure of the complex formed by Wolbachia cytoplasmic incompatibility factors CidAwMel(ST) and CidBND1-ND2 from wPip(Pel)
Components
  • ULP_PROTEASE domain-containing protein
  • bacteria factor 4,CidA I(Zeta/1) protein
KeywordsPROTEIN BINDING / Wolbachia / cytoplasmic incompatibility / antitoxin
Function / homologyUbiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Ulp1 protease family, C-terminal catalytic domain / cysteine-type peptidase activity / Papain-like cysteine peptidase superfamily / proteolysis / CidA I(Zeta/1) protein / ULP_PROTEASE domain-containing protein / Cytoplasmic incompatibility factor CifA
Function and homology information
Biological speciesWolbachia endosymbiont of Culex quinquefasciatus Pel (bacteria)
Wolbachia endosymbiont of Drosophila melanogaster (bacteria)
Wolbachia endosymbiont of Culex pipiens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 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 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ULP_PROTEASE domain-containing protein
B: bacteria factor 4,CidA I(Zeta/1) protein


Theoretical massNumber of molelcules
Total (without water)144,8382
Polymers144,8382
Non-polymers00
Water11,584643
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint8 kcal/mol
Surface area46980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.357, 98.690, 184.847
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ULP_PROTEASE domain-containing protein / bacteria factor 3


Mass: 88873.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wolbachia endosymbiont of Culex quinquefasciatus Pel (bacteria)
Strain: wPip / Gene: WP0283 / Production host: Escherichia coli (E. coli) / References: UniProt: B3CP63
#2: Protein bacteria factor 4,CidA I(Zeta/1) protein


Mass: 55964.977 Da / Num. of mol.: 1 / Mutation: R7K,L47Y,P93R,Q288R,Y295S,N299D,G347E,E393R,I397L
Source method: isolated from a genetically manipulated source
Details: Chimeric protein CidASTwMel
Source: (gene. exp.) Wolbachia endosymbiont of Drosophila melanogaster (bacteria), (gene. exp.) Wolbachia endosymbiont of Culex pipiens (bacteria)
Gene: WD_0631 / Production host: Escherichia coli (E. coli) / References: UniProt: Q73HD5, UniProt: A0A5B8WHG9
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 643 / 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: 2.64 Å3/Da / Density % sol: 53.36 %
Crystal growTemperature: 289.15 K / Method: batch mode
Details: 5% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.1M HEPES pH 7.5, 10% w/v Polyethylene glycol 10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 80310 / % possible obs: 98.8 % / Redundancy: 10.8 % / Biso Wilson estimate: 38.53 Å2 / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.054 / Rrim(I) all: 0.184 / Χ2: 1.01 / Net I/σ(I): 5.1 / Num. measured all: 868431
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.15-2.196.21.04835240.4820.4061.1311.00488
2.19-2.236.90.9737110.5590.3611.041.00993
2.23-2.277.20.84938830.6820.3130.9081.00796.4
2.27-2.328.10.79739830.7570.280.8481.00499.2
2.32-2.379.40.71940150.840.2370.7591.00999.8
2.37-2.42110.68240100.8780.2110.7151.001100
2.42-2.4811.50.63840300.8990.1940.6671.004100
2.48-2.5511.90.56340170.930.1690.5881.008100
2.55-2.6211.80.48940100.9390.1480.5111.003100
2.62-2.7111.60.41140470.9530.1250.431.002100
2.71-2.8110.90.34640410.9660.1090.3641.002100
2.81-2.9211.70.29140470.9750.0880.3041.016100
2.92-3.0512.70.25540510.9830.0740.2651.026100
3.05-3.2112.50.21240300.9870.0620.2210.998100
3.21-3.4112.20.17940960.9890.0530.1871.001100
3.41-3.6811.40.1540760.9910.0460.1571.025100
3.68-4.0512.30.13240800.9930.0390.1381.005100
4.05-4.6312.60.11841390.9950.0340.1231.017100
4.63-5.8311.40.10941720.9940.0330.1141.026100
5.83-5011.70.08743480.9970.0270.0911.01899.7

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7FIV

7fiv


Resolution: 2.16→31.62 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2196 2000 2.5 %
Rwork0.192 78142 -
obs0.1926 80142 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.96 Å2 / Biso mean: 49.7114 Å2 / Biso min: 21.85 Å2
Refinement stepCycle: final / Resolution: 2.16→31.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9354 0 0 643 9997
Biso mean---48.43 -
Num. residues----1151
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.16-2.210.32231200.30914694481484
2.21-2.270.31491370.28815347548495
2.27-2.340.33081430.26815553569699
2.34-2.420.30321430.251156195762100
2.42-2.50.26331430.24755845727100
2.5-2.60.26141440.234156305774100
2.6-2.720.27231440.218256375781100
2.72-2.860.23951440.218156385782100
2.86-3.040.2611450.215656665811100
3.04-3.280.21631450.198456625807100
3.28-3.610.20521460.185556905836100
3.61-4.130.19471460.16157205866100
4.13-5.20.17621470.144457835930100
5.2-31.620.17571530.16625919607299
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)
11.31740.5228-0.56882.5892-0.91091.5323-0.0428-0.0964-0.26110.1466-0.0434-0.00790.190.01710.07610.20490.0050.0240.22930.00420.24157.47082.2628113.2833
20.4537-0.5804-0.50111.50861.73542.08070.127-0.03570.24450.0518-0.11770.1345-0.1442-0.1532-0.01880.3109-0.01810.0620.287-0.00850.401349.045634.3544113.0043
32.1666-0.5461-0.08241.93570.15071.57960.1071-0.29410.41320.1537-0.07570.0426-0.20760.0104-0.03130.4148-0.09320.08520.3659-0.08230.384754.480244.0769128.3268
46.63950.3790.35977.04897.30317.5742-0.00420.2491-0.030.2958-0.09850.48710.4953-0.47740.10290.3099-0.0667-0.08370.39180.22340.609444.63945.44989.2307
52.26010.76521.32091.18681.08442.1778-0.215-0.0170.5933-0.19820.18390.8091-0.476-0.59310.02350.42320.0524-0.0380.47310.21320.820845.49558.326490.9196
62.37540.6764-0.15120.3878-0.63772.44710.062-0.22990.34550.1853-0.09820.4226-1.2894-0.4370.03710.68170.08720.08780.37510.07960.937152.331270.6213113.6456
70.4053-0.8904-1.15043.12013.40654.5640.04850.03630.2690.15810.13890.1034-0.10910.0333-0.18510.3560.0073-0.00290.35880.07960.662962.8361.3717101.1845
83.2480.6075-0.6287.69311.83412.3671-0.23120.3410.177-0.20720.4775-0.56390.08740.0912-0.26020.2628-0.0554-0.0540.41020.07620.329368.97541.126182.7323
91.8926-0.28120.14452.3064-0.28771.1966-0.06530.56320.0355-0.30030.0866-0.10480.09710.338-0.02120.2732-0.02170.00110.50490.00210.17457.110619.738279.0351
106.6257-0.04260.31318.1066-0.14093.49240.05080.2007-0.598-0.12880.13540.44110.2147-0.1071-0.17740.2297-0.0349-0.03170.33930.04860.300746.30513.044481.8914
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 337 )A2 - 337
2X-RAY DIFFRACTION2chain 'A' and (resid 338 through 448 )A338 - 448
3X-RAY DIFFRACTION3chain 'A' and (resid 449 through 759 )A449 - 759
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 45 )B4 - 45
5X-RAY DIFFRACTION5chain 'B' and (resid 46 through 106 )B46 - 106
6X-RAY DIFFRACTION6chain 'B' and (resid 107 through 131 )B107 - 131
7X-RAY DIFFRACTION7chain 'B' and (resid 132 through 194 )B132 - 194
8X-RAY DIFFRACTION8chain 'B' and (resid 195 through 286 )B195 - 286
9X-RAY DIFFRACTION9chain 'B' and (resid 287 through 397 )B287 - 397
10X-RAY DIFFRACTION10chain 'B' and (resid 398 through 421 )B398 - 421

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