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

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Basic information

Entry
Database: PDB / ID: 7esx
TitleCrystal structure of Wolbachia cytoplasmic incompatibility factor CidA from wPip
ComponentsBacteria factor 1
KeywordsANTITOXIN / Wolbachia / cytoplasmic incompatibility
Function / homologyCidA_IV beta/2 protein
Function and homology information
Biological speciesWolbachia pipientis subsp. Culex pipiens
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 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: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Structural and mechanistic insights into the complexes formed by Wolbachia cytoplasmic incompatibility factors.
Authors: Xiao, Y. / Chen, H. / Wang, H. / Zhang, M. / Chen, X. / Berk, J.M. / Zhang, L. / Wei, Y. / Li, W. / Cui, W. / Wang, F. / Wang, Q. / Cui, C. / Li, T. / Chen, C. / Ye, S. / Zhang, L. / Ji, X. ...Authors: Xiao, Y. / Chen, H. / Wang, H. / Zhang, M. / Chen, X. / Berk, J.M. / Zhang, L. / Wei, Y. / Li, W. / Cui, W. / Wang, F. / Wang, Q. / Cui, C. / Li, T. / Chen, C. / Ye, S. / Zhang, L. / Ji, X. / Huang, J. / Wang, W. / Wang, Z. / Hochstrasser, M. / Yang, H.
History
DepositionMay 12, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bacteria factor 1
B: Bacteria factor 1


Theoretical massNumber of molelcules
Total (without water)114,9652
Polymers114,9652
Non-polymers00
Water14,466803
1
A: Bacteria factor 1


Theoretical massNumber of molelcules
Total (without water)57,4821
Polymers57,4821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bacteria factor 1


Theoretical massNumber of molelcules
Total (without water)57,4821
Polymers57,4821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.671, 63.376, 66.716
Angle α, β, γ (deg.)82.590, 70.210, 89.370
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(CHAIN A AND (RESID 2 THROUGH 122 OR (RESID 123...
21(CHAIN B AND (RESID 2 THROUGH 276 OR (RESID 277...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROPROPRO(CHAIN A AND (RESID 2 THROUGH 122 OR (RESID 123...AA22
12ARGARGARGARG(CHAIN A AND (RESID 2 THROUGH 122 OR (RESID 123...AA123123
13PROPROLYSLYS(CHAIN A AND (RESID 2 THROUGH 122 OR (RESID 123...AA2 - 4282 - 428
14PROPROLYSLYS(CHAIN A AND (RESID 2 THROUGH 122 OR (RESID 123...AA2 - 4282 - 428
15PROPROLYSLYS(CHAIN A AND (RESID 2 THROUGH 122 OR (RESID 123...AA2 - 4282 - 428
16PROPROLYSLYS(CHAIN A AND (RESID 2 THROUGH 122 OR (RESID 123...AA2 - 4282 - 428
21PROPROPROPRO(CHAIN B AND (RESID 2 THROUGH 276 OR (RESID 277...BB22
22GLUGLUGLUGLU(CHAIN B AND (RESID 2 THROUGH 276 OR (RESID 277...BB277277
23PROPROLEULEU(CHAIN B AND (RESID 2 THROUGH 276 OR (RESID 277...BB2 - 4312 - 431
24PROPROLEULEU(CHAIN B AND (RESID 2 THROUGH 276 OR (RESID 277...BB2 - 4312 - 431
25PROPROLEULEU(CHAIN B AND (RESID 2 THROUGH 276 OR (RESID 277...BB2 - 4312 - 431
26PROPROLEULEU(CHAIN B AND (RESID 2 THROUGH 276 OR (RESID 277...BB2 - 4312 - 431

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Components

#1: Protein Bacteria factor 1


Mass: 57482.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wolbachia pipientis subsp. Culex pipiens (strain wPip) (bacteria)
Strain: wPip / Gene: WP0282 / Production host: Escherichia coli (E. coli) / References: UniProt: B3CP62
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 803 / 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: 1.94 Å3/Da / Density % sol: 36.71 %
Crystal growTemperature: 289 K / Method: batch mode
Details: 0.1M Tris pH 8.0, 30% w/v polyethylene glycol monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97776 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: May 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 76435 / % possible obs: 95.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.057 / Rrim(I) all: 0.106 / Χ2: 1.955 / Net I/σ(I): 26.4 / Num. measured all: 267156
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.655 / Num. unique obs: 3846 / CC1/2: 0.994 / Rpim(I) all: 0.036 / Rrim(I) all: 0.067 / Χ2: 3.388 / % possible all: 95.2

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
PHENIXmodel building
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→47.47 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0.09 / Phase error: 20.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.198 1982 2.62 %
Rwork0.165 73537 -
obs0.166 75519 94.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.09 Å2 / Biso mean: 32.01 Å2 / Biso min: 8.65 Å2
Refinement stepCycle: final / Resolution: 1.8→47.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6885 0 0 803 7688
Biso mean---37.78 -
Num. residues----841
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3989X-RAY DIFFRACTIONPOSITIONAL0
12B3989X-RAY DIFFRACTIONPOSITIONAL0
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.801-1.83190.2312940.2003341888
1.8319-1.86520.22771000.1908361292
1.8652-1.90110.2583970.1949359792
1.9011-1.93990.2162980.1943359393
1.9399-1.98210.2526980.1875368094
1.9821-2.02820.2593990.1836370295
2.0282-2.07890.2095990.1735366595
2.0789-2.13510.2391000.1722371495
2.1351-2.1980.20431020.1622374895
2.198-2.26890.18871000.1643370595
2.2689-2.350.21031010.164375396
2.35-2.44410.1991990.162369995
2.4441-2.55530.17521000.1644372595
2.5553-2.690.23681020.1741375596
2.69-2.85860.19841000.1751371396
2.8586-3.07920.21551000.1761373096
3.0792-3.3890.2087980.1701364593
3.389-3.87920.19121010.1528372996
3.8792-4.88660.1486960.1379361893
4.8866-47.470.1725980.1565373695
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)
16.40675.14574.7537.02715.22244.6949-0.20920.3396-0.134-0.23430.3419-0.1068-0.33780.5879-0.11250.1101-0.020.0350.1748-0.00210.114916.321-24.00445.001
21.85640.32061.2571.8539-0.07786.6929-0.15120.3405-0.0546-0.6990.41090.5407-0.1025-0.3255-0.00030.275-0.098-0.0750.1522-0.01450.03995.679-24.7935.615
37.5476-1.28880.33753.9359-0.70113.2038-0.0746-0.7687-0.32671.17150.0623-0.44960.07870.0795-0.01060.1816-0.0195-0.01110.23010.00570.14911.576-26.30852.249
46.6388-3.58864.25976.382-3.40457.12980.04730.4392-0.2663-0.3779-0.02960.08140.12190.0404-0.00760.1779-0.04520.01620.1453-0.05090.10874.972-33.65240.329
56.4227-1.8562-1.99345.31691.26635.2137-0.04920.0926-0.5723-0.02060.06940.03120.3947-0.119-0.02780.1518-0.0606-0.02510.1152-0.00880.11920.498-37.86550.862
64.12361.29294.91347.87471.19157.52610.1521-0.4373-0.73190.21760.0733-0.73321.2259-0.1634-0.2060.3369-0.05560.0380.21760.02460.2146-0.902-41.56964.646
76.4531-0.0193-1.34450.0658-0.34032.22930.86-0.9759-2.00260.1597-0.0858-0.37310.47330.0115-0.54680.9046-0.1062-0.34450.41990.15760.66926.061-44.02275.154
84.4525-3.8125-6.18466.93076.56249.06190.4054-1.7818-0.3908-0.05550.1315-1.44380.81421.3118-0.05040.886-0.2847-0.03010.74380.36180.72970.128-44.97583.021
98.76135.1503-4.85758.6477-6.56647.9509-0.0714-0.51660.03320.5901-0.2907-0.08480.03520.55840.36520.4181-0.0515-0.01630.27460.03380.1564-1.087-35.15572.943
102.6207-2.6328-0.443.6924-1.19932.79610.1767-1.68830.15470.77090.1305-0.2928-0.32350.064-0.32590.2425-0.0564-0.04880.406-0.01880.1497-1.905-27.40962.394
115.93460.9001-1.14553.8886-0.32026.27340.1001-0.5097-0.48640.62940.35180.89950.4198-0.5884-0.39780.3027-0.06550.08340.27950.09080.2447-11.481-32.81164.784
125.50180.27042.37786.18480.30685.9995-0.0181-0.13580.2180.110.05150.2239-0.0033-0.0173-0.03820.0993-0.02280.02550.12890.01340.0861-11.527-23.0253.356
136.71654.5755-0.59826.01540.58522.19570.1861-0.27580.1734-0.0179-0.15320.6668-0.1834-0.6265-0.00680.1154-0.0163-0.0150.25320.0540.2328-17.121-14.62349.057
143.55031.71860.62066.71031.26893.7191-0.16250.1983-0.06990.04580.2257-0.1761-0.08320.2018-0.060.0854-0.0147-0.00140.18310.03630.1216-4.263-13.43647.8
156.95873.32772.66826.4907-0.79124.97950.01940.24240.3175-0.2480.64711.6135-0.0723-1.2884-0.26290.17860.03880.00710.45110.2230.4459-16.498-6.23941.833
165.1178-4.4387-5.86954.34975.17758.5316-0.1447-0.6320.72070.34230.5213-0.707-0.25040.6305-0.24990.1603-0.0268-0.00650.17960.03590.1929-2.732-4.85444.699
177.9871-2.0530.28588.2983-1.9626.08110.04820.65610.1137-0.7727-0.17410.02760.0597-0.04170.04670.1718-0.06070.01540.23060.02380.118-5.574-9.27434.169
183.8991-4.3761-1.48426.54010.14052.05270.30181.30860.1959-0.9891-0.00791.2907-0.5823-0.9453-0.14120.3990.1184-0.05460.52720.1740.5139-11.2015.07934.216
195.4626-2.8793-1.93417.75742.08683.04490.00450.20730.06770.187-0.0654-0.11330.2516-0.14630.06120.1186-0.02410.03040.11380.05660.10765.993-5.64733.943
203.9562-0.9037-0.91432.5235-0.03272.06130.1024-0.06440.36020.01580.0941-0.0924-0.0566-0.0229-0.15290.1103-0.00480.02210.12680.05680.17811.2050.13330.201
215.2952-1.9415-1.61527.30250.90033.90410.19880.55450.1272-0.3937-0.0870.03360.0704-0.0507-0.0940.21650.03540.01360.2870.09810.191211.861-2.22220.938
226.6941-1.21841.37563.1627-0.80124.1342-0.0029-0.30270.77920.10270.4087-0.7602-0.2569-0.1576-0.24160.1982-0.0090.08450.0891-0.00640.522418.0989.00630.372
237.4439-1.67681.8696.663-1.96593.40240.3155-0.9906-0.15190.7466-0.3696-1.0251-0.09340.87640.11840.2735-0.02-0.10770.41220.09460.518126.09-6.59534.368
245.9298-0.38730.32632.6702-2.32427.7302-0.0141.19240.5511-1.0112-0.1867-1.1661-0.2890.61050.26460.3697-0.05460.08730.35940.0950.446122.0022.38121.481
255.46177.20415.1369.65637.07285.09310.1969-0.64450.54330.4365-0.47370.4758-0.1472-0.82530.24380.28950.06290.07380.3716-0.00810.2443-21.463-10.58619.939
266.56574.90310.51956.28721.18726.8615-0.0879-0.0842-0.0272-0.06570.02760.20560.1521-0.77290.06090.20390.03610.01620.20010.01550.1065-23.642-21.6611.297
274.06280.52991.10876.80430.1855.5342-0.0767-0.10650.33280.01360.10230.2925-0.4561-0.3682-0.01030.19460.06220.05910.23110.05430.1363-20.015-11.1849.06
288.7038-0.3016-1.51475.81940.32383.47050.08660.33830.6145-0.3578-0.02580.3336-0.5258-0.3033-0.03880.34430.0175-0.02920.18130.03120.1443-15.417-7.021-0.881
291.6912-0.37211.19614.9114-0.96271.6024-0.42310.21930.858-0.17470.1196-0.8675-0.89930.35140.14190.6732-0.1401-0.04150.26490.04310.4915-0.3341.608-1.099
305.3434-0.9074-0.93926.50642.1754.7643-0.0161-0.06620.1423-0.09830.1131-0.2868-0.21780.1026-0.10250.1777-0.03260.01690.127-0.00540.0723-0.606-19.1341.731
317.42170.34720.70262.65441.24557.94020.03320.2385-0.00840.160.25-0.49310.34761.0037-0.27530.25910.0256-0.01210.3096-0.02420.19963.173-29.1994.166
326.43760.1019-0.33324.61054.31454.6922-0.1176-0.67960.17310.11390.1953-0.056-0.38910.124-0.07290.30250.03150.01280.28160.03620.1138-5.655-24.3511.629
334.5933-0.83234.66952.2256-1.4655.02820.23070.0773-0.3177-0.5099-0.122-0.42860.84740.8696-0.25240.34630.08780.02670.3387-0.00420.20161.178-38.47110.154
344.6581-4.29272.01774.7522-1.89746.4696-0.1063-0.72760.57310.42250.1758-0.5337-0.4910.25690.02390.3015-0.04910.0040.2423-0.00690.1366-4.036-30.88820.783
356.9852-4.23910.55174.0973-2.05542.71540.30750.3206-0.207-0.3784-0.21580.28820.1318-0.1798-0.09690.180.00860.02830.18760.00450.0886-12.132-34.63514.109
366.7756-0.54741.2685.98521.99368.67290.0580.6484-1.2051-0.7806-0.0337-0.48930.87020.5097-0.06530.40750.0830.1070.304-0.04730.3592-3.83-48.78218.497
378.5181-4.04570.18764.9638-1.07172.7666-0.001-0.0660.1884-0.04640.04770.0279-0.15530.0123-0.04380.139-0.01130.02810.13580.01990.0454-17.167-33.24125.022
382.9557-0.023-1.39144.20391.46766.6574-0.0517-0.6506-0.29780.2614-0.0841-0.16090.35330.36310.06190.14680.0220.00110.28110.09280.1949-12.284-43.44234.474
397.719-1.81082.42776.5608-2.00018.19920.00170.14030.4569-0.0813-0.06660.2908-0.1906-0.10660.04420.14310.020.04290.1013-0.00650.1258-29.172-30.07429.659
408.9136-5.63663.91168.6628-3.75724.30770.05470.1051-0.3589-0.2267-0.20730.340.16840.08960.09740.1687-0.01020.03160.1811-0.02410.1881-28.44-41.81529.168
415.2081-3.8815-1.13858.5456-0.52713.4352-0.1211-0.51150.25070.34840.0388-0.5154-0.16350.35440.12530.1695-0.0524-0.03660.25150.00810.1322-24.007-34.37741.564
424.90044.29960.14948.97010.25425.76770.1357-0.0932-0.61120.2662-0.24870.13930.27050.02660.06410.12530.01280.03190.21260.01260.245-32.205-41.99538.75
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:18 )A2 - 18
2X-RAY DIFFRACTION2( CHAIN A AND RESID 19:38 )A19 - 38
3X-RAY DIFFRACTION3( CHAIN A AND RESID 39:53 )A39 - 53
4X-RAY DIFFRACTION4( CHAIN A AND RESID 54:76 )A54 - 76
5X-RAY DIFFRACTION5( CHAIN A AND RESID 77:110 )A77 - 110
6X-RAY DIFFRACTION6( CHAIN A AND RESID 111:122 )A111 - 122
7X-RAY DIFFRACTION7( CHAIN A AND RESID 123:127 )A123 - 127
8X-RAY DIFFRACTION8( CHAIN A AND RESID 128:135 )A128 - 135
9X-RAY DIFFRACTION9( CHAIN A AND RESID 136:154 )A136 - 154
10X-RAY DIFFRACTION10( CHAIN A AND RESID 155:159 )A155 - 159
11X-RAY DIFFRACTION11( CHAIN A AND RESID 160:173 )A160 - 173
12X-RAY DIFFRACTION12( CHAIN A AND RESID 174:198 )A174 - 198
13X-RAY DIFFRACTION13( CHAIN A AND RESID 199:213 )A199 - 213
14X-RAY DIFFRACTION14( CHAIN A AND RESID 214:232 )A214 - 232
15X-RAY DIFFRACTION15( CHAIN A AND RESID 233:245 )A233 - 245
16X-RAY DIFFRACTION16( CHAIN A AND RESID 246:259 )A246 - 259
17X-RAY DIFFRACTION17( CHAIN A AND RESID 260:276 )A260 - 276
18X-RAY DIFFRACTION18( CHAIN A AND RESID 277:290 )A277 - 290
19X-RAY DIFFRACTION19( CHAIN A AND RESID 291:324 )A291 - 324
20X-RAY DIFFRACTION20( CHAIN A AND RESID 325:364 )A325 - 364
21X-RAY DIFFRACTION21( CHAIN A AND RESID 365:385 )A365 - 385
22X-RAY DIFFRACTION22( CHAIN A AND RESID 386:404 )A386 - 404
23X-RAY DIFFRACTION23( CHAIN A AND RESID 406:414 )A406 - 414
24X-RAY DIFFRACTION24( CHAIN A AND RESID 415:428 )A415 - 428
25X-RAY DIFFRACTION25( CHAIN B AND RESID 2:18 )B2 - 18
26X-RAY DIFFRACTION26( CHAIN B AND RESID 19:38 )B19 - 38
27X-RAY DIFFRACTION27( CHAIN B AND RESID 39:76 )B39 - 76
28X-RAY DIFFRACTION28( CHAIN B AND RESID 77:110 )B77 - 110
29X-RAY DIFFRACTION29( CHAIN B AND RESID 111:173 )B111 - 173
30X-RAY DIFFRACTION30( CHAIN B AND RESID 174:198 )B174 - 198
31X-RAY DIFFRACTION31( CHAIN B AND RESID 199:213 )B199 - 213
32X-RAY DIFFRACTION32( CHAIN B AND RESID 214:232 )B214 - 232
33X-RAY DIFFRACTION33( CHAIN B AND RESID 233:245 )B233 - 245
34X-RAY DIFFRACTION34( CHAIN B AND RESID 246:259 )B246 - 259
35X-RAY DIFFRACTION35( CHAIN B AND RESID 260:273 )B260 - 273
36X-RAY DIFFRACTION36( CHAIN B AND RESID 274:290 )B274 - 290
37X-RAY DIFFRACTION37( CHAIN B AND RESID 291:324 )B291 - 324
38X-RAY DIFFRACTION38( CHAIN B AND RESID 325:345 )B325 - 345
39X-RAY DIFFRACTION39( CHAIN B AND RESID 346:364 )B346 - 364
40X-RAY DIFFRACTION40( CHAIN B AND RESID 365:385 )B365 - 385
41X-RAY DIFFRACTION41( CHAIN B AND RESID 386:414 )B386 - 414
42X-RAY DIFFRACTION42( CHAIN B AND RESID 415:431 )B415 - 431

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