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

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Basic information

Entry
Database: PDB / ID: 7fiv
TitleCrystal structure of the complex formed by Wolbachia cytoplasmic incompatibility factors CidA and CidBND1-ND2 from wPip(Tunis)
Components
  • CidA_I gamma/2 protein
  • CidB_I b/2 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 / CidA_I gamma/2 protein / CidB_I b/2 protein
Function and homology information
Biological speciesWolbachia endosymbiont of Culex pipiens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 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

Downloads & links

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Assembly

Deposited unit
A: CidA_I gamma/2 protein
B: CidB_I b/2 protein


Theoretical massNumber of molelcules
Total (without water)146,3942
Polymers146,3942
Non-polymers00
Water3,297183
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)181.577, 181.577, 54.596
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein CidA_I gamma/2 protein


Mass: 57510.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wolbachia endosymbiont of Culex pipiens (bacteria)
Gene: cidA / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2K9VS01
#2: Protein CidB_I b/2 protein


Mass: 88883.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wolbachia endosymbiont of Culex pipiens (bacteria)
Gene: cidB / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2K9VS18
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 3.09 Å3/Da / Density % sol: 60.24 %
Crystal growTemperature: 289.15 K / Method: batch mode
Details: 0.1M BICINE pH 8.5, 15% w/v Polyethylene glycol 1500

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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: Oct 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 56251 / % possible obs: 100 % / Redundancy: 11.1 % / Biso Wilson estimate: 55.31 Å2 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.058 / Rrim(I) all: 0.199 / Χ2: 1.03 / Net I/σ(I): 4.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.646.81.31227720.4110.5061.4141.00899.6
2.64-2.698.51.18227880.5390.4131.2551.022100
2.69-2.749.91.10128030.6150.3591.161.058100
2.74-2.810.80.96527610.7370.3031.0121.033100
2.8-2.86110.82927980.7640.2570.8691.067100
2.86-2.9311.10.74427670.8170.2310.781.058100
2.93-310.90.61528010.8630.1930.6451.066100
3-3.0810.40.54527810.8810.1760.5741.066100
3.08-3.1710.70.45727880.9090.1440.4791.073100
3.17-3.2811.50.3728160.940.1130.3871.04100
3.28-3.3911.70.3128010.9650.0930.3241.007100
3.39-3.5311.70.2727870.9710.0810.2821.006100
3.53-3.6911.80.2328170.9810.070.2411.019100
3.69-3.8811.60.20128330.9850.0610.211.035100
3.88-4.1311.30.18427940.9820.0580.1930.999100
4.13-4.4512.30.15728210.990.0460.1631.025100
4.45-4.8912.80.14328260.9920.0410.1491.023100
4.89-5.612.60.13628550.9930.040.1421.006100
5.6-7.0512.10.13128640.9920.0390.1371.002100
7.05-5011.40.08929780.9970.0270.0931.005100

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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: 7ESY

7esy


Resolution: 2.59→35.61 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2443 1998 3.56 %
Rwork0.1963 54172 -
obs0.198 56170 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 160.76 Å2 / Biso mean: 71.8334 Å2 / Biso min: 25.22 Å2
Refinement stepCycle: final / Resolution: 2.59→35.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9156 0 0 183 9339
Biso mean---56.8 -
Num. residues----1149
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 (%)
2.59-2.650.35281420.32273718386098
2.65-2.720.33441390.287238644003100
2.72-2.80.29211390.28438183957100
2.8-2.890.32971460.266338704016100
2.89-30.3541430.258438363979100
3-3.120.31341400.236838543994100
3.12-3.260.27081430.231238594002100
3.26-3.430.2621450.210538694014100
3.43-3.650.26721440.190638954039100
3.65-3.930.2061410.175638473988100
3.93-4.320.19851460.170238744020100
4.32-4.950.22841420.154839264068100
4.95-6.220.22781450.185739284073100
6.23-35.610.19761430.1664014415799
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)
11.72510.74910.39644.1869-0.52771.32290.03950.06380.2790.0483-0.1971-0.3773-0.1260.44130.14820.3472-0.10240.01820.55260.07070.4475-48.136428.85240.9335
23.2413-0.2618-0.30221.95560.04561.2427-0.15010.1831.3759-0.0171-0.09420.2856-0.44520.18320.17640.7055-0.16-0.07930.52620.1511.241-67.483954.4241-9.6153
34.0889-2.22611.49063.8233-0.06811.72720.08820.23550.36680.00720.06950.7091-0.2488-0.4063-0.14080.41940.12550.05560.54210.12790.7798-109.235334.7742-12.7423
46.9601-0.2072-1.39581.0984-0.89282.57460.0655-0.0532-0.0870.32310.20750.3551-0.6453-0.7454-0.23750.66510.18350.14750.72320.0780.9829-119.022337.2884-2.5075
56.6426-0.43460.05212.8166-0.01433.36570.0493-0.00010.81860.1752-0.05670.0532-0.28780.0506-0.00220.3564-0.01880.01680.27890.07880.4757-86.097536.2557-6.7492
62.1251-0.42560.49761.3432-0.62070.81020.1524-0.16190.47170.1177-0.106-0.0261-0.1470.1215-0.0330.4112-0.04540.01740.3867-0.00920.2963-72.240620.16035.095
76.955-4.13872.68285.2791-0.58973.3891-0.0858-0.5898-0.26070.34690.11960.42080.23940.1584-0.04670.4595-0.0560.00680.39260.07620.1997-68.93742.448915.2699
80.89860.03811.22481.59570.25164.91650.0892-0.0827-0.06760.2197-0.0719-0.20.34970.6525-0.01880.36960.01410.01780.48610.02030.2913-65.36673.05047.6895
93.0084-0.74531.32362.46050.09972.4401-0.0965-0.08750.1887-0.12860.06240.5138-0.1813-0.24190.00020.415-0.0195-0.03040.39610.03130.3252-87.022912.2438-10.2132
104.32380.71590.32324.8373-1.8485.6840.11640.2144-0.1537-0.38120.02320.16210.2296-0.0429-0.1380.35380.00910.03220.3227-0.09360.1734-79.06834.0875-15.4397
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 196 )A2 - 196
2X-RAY DIFFRACTION2chain 'A' and (resid 197 through 427 )A197 - 427
3X-RAY DIFFRACTION3chain 'B' and (resid 4 through 168 )B4 - 168
4X-RAY DIFFRACTION4chain 'B' and (resid 169 through 235 )B169 - 235
5X-RAY DIFFRACTION5chain 'B' and (resid 236 through 365 )B236 - 365
6X-RAY DIFFRACTION6chain 'B' and (resid 366 through 462 )B366 - 462
7X-RAY DIFFRACTION7chain 'B' and (resid 463 through 505 )B463 - 505
8X-RAY DIFFRACTION8chain 'B' and (resid 506 through 604 )B506 - 604
9X-RAY DIFFRACTION9chain 'B' and (resid 605 through 662 )B605 - 662
10X-RAY DIFFRACTION10chain 'B' and (resid 663 through 758 )B663 - 758

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