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Basic information

Entry
Database: PDB / ID: 7esz
TitleCrystal structure of the complex formed by Wolbachia cytoplasmic incompatibility factors CinA and CinB with Mn2+ from wPip
Components
  • BACTERIA FACTOR A
  • BACTERIA FACTOR B
KeywordsPROTEIN BINDING / Wolbachia / Nuclease / Antitoxin / Toxin
Function / homology: / Uncharacterized protein / ANK_REP_REGION domain-containing protein
Function and homology information
Biological speciesWolbachia pipientis subsp. Culex pipiens
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.476 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

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Assembly

Deposited unit
A: BACTERIA FACTOR B
B: BACTERIA FACTOR A
C: BACTERIA FACTOR B
D: BACTERIA FACTOR A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)273,9666
Polymers273,8564
Non-polymers1102
Water1,69394
1
A: BACTERIA FACTOR B
B: BACTERIA FACTOR A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,9833
Polymers136,9282
Non-polymers551
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-5 kcal/mol
Surface area43340 Å2
MethodPISA
2
C: BACTERIA FACTOR B
D: BACTERIA FACTOR A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,9833
Polymers136,9282
Non-polymers551
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-2 kcal/mol
Surface area44150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.466, 86.380, 93.018
Angle α, β, γ (deg.)110.060, 91.860, 115.380
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 6 through 86 or (resid 87...
21(chain C and (resid 6 through 125 or (resid 126...
12(chain B and (resid 3 through 22 or (resid 23...
22(chain D and (resid 3 through 86 or (resid 87...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LYSLYSLEULEU(chain A and (resid 6 through 86 or (resid 87...AA6 - 866 - 86
121LYSLYSLYSLYS(chain A and (resid 6 through 86 or (resid 87...AA8787
131ASNASNASNASN(chain A and (resid 6 through 86 or (resid 87...AA4 - 6944 - 694
141ASNASNASNASN(chain A and (resid 6 through 86 or (resid 87...AA4 - 6944 - 694
151ASNASNASNASN(chain A and (resid 6 through 86 or (resid 87...AA4 - 6944 - 694
211LYSLYSTRPTRP(chain C and (resid 6 through 125 or (resid 126...CC6 - 1256 - 125
221LYSLYSLYSLYS(chain C and (resid 6 through 125 or (resid 126...CC126126
231LYSLYSASPASP(chain C and (resid 6 through 125 or (resid 126...CC6 - 7006 - 700
112SERSERGLYGLY(chain B and (resid 3 through 22 or (resid 23...BB3 - 223 - 22
122ASPASPASPASP(chain B and (resid 3 through 22 or (resid 23...BB2323
132SERSERILEILE(chain B and (resid 3 through 22 or (resid 23...BB3 - 4163 - 416
142SERSERILEILE(chain B and (resid 3 through 22 or (resid 23...BB3 - 4163 - 416
152SERSERILEILE(chain B and (resid 3 through 22 or (resid 23...BB3 - 4163 - 416
162SERSERILEILE(chain B and (resid 3 through 22 or (resid 23...BB3 - 4163 - 416
212SERSERASNASN(chain D and (resid 3 through 86 or (resid 87...DD3 - 863 - 86
222LYSLYSLYSLYS(chain D and (resid 3 through 86 or (resid 87...DD8787
232SERSERLYSLYS(chain D and (resid 3 through 86 or (resid 87...DD3 - 4133 - 413
242SERSERLYSLYS(chain D and (resid 3 through 86 or (resid 87...DD3 - 4133 - 413
252SERSERLYSLYS(chain D and (resid 3 through 86 or (resid 87...DD3 - 4133 - 413
262SERSERLYSLYS(chain D and (resid 3 through 86 or (resid 87...DD3 - 4133 - 413

NCS ensembles :
ID
1
2

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Components

#1: Protein BACTERIA FACTOR B


Mass: 84330.586 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: WP0295 / Production host: Escherichia coli (E. coli) / References: UniProt: B3CP74
#2: Protein BACTERIA FACTOR A


Mass: 52597.383 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: WP0294 / Production host: Escherichia coli (E. coli) / References: UniProt: B3CP73
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.11 Å3/Da / Density % sol: 41.79 %
Crystal growTemperature: 289.15 K / Method: batch mode
Details: buffer A (0.2M L-Proline, 0.1M Hepes pH 7.5, 24% w/v polyethylene glycol 1500): buffer B (0.1M citric acid pH 3.5, 34% v/v polyethylene glycol 200) = 4:1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97876 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97876 Å / Relative weight: 1
ReflectionResolution: 2.476→50 Å / Num. obs: 73644 / % possible obs: 97.1 % / Redundancy: 3 % / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.144 / Rrim(I) all: 0.211 / Χ2: 2.14 / Net I/σ(I): 11.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Χ2% possible allRpim(I) allRmerge(I) obsRrim(I) all
2.5-2.542.836980.1060.54196.6
2.54-2.592.937100.1060.54496.3
2.59-2.642.935790.1360.55196.4
2.64-2.692.837000.1680.61296.80.93
2.69-2.752.637070.1660.64597.20.958
2.75-2.822.736710.2310.67197.50.745
2.82-2.892.936750.3810.72897.60.5850.847
2.89-2.963.237320.5970.88597.80.4640.7180.857
2.96-3.053.237150.6510.94297.80.3690.5610.674
3.05-3.153.236860.8281.20497.80.2720.4170.5
3.15-3.263.237210.8421.41798.20.2190.3340.401
3.26-3.393.236860.8731.73998.10.1920.290.35
3.39-3.553.137370.92.32998.10.1660.2510.302
3.55-3.733.137630.9212.90897.80.1450.2150.26
3.73-3.972.836640.9053.48997.60.140.190.238
3.97-4.272.837150.9363.85697.60.120.1630.203
4.27-4.73.236350.9654.11996.30.0860.1290.156
4.7-5.383.236610.974.15496.30.0820.1240.149
5.38-6.783.236300.9674.55496.60.0830.1240.15
6.78-50335590.9836.24593.40.0550.0790.096

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
PHENIXmodel building
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.476→41.071 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 28.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2502 3672 5 %
Rwork0.198 69700 -
obs0.2006 73372 93.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 148.67 Å2 / Biso mean: 53.8624 Å2 / Biso min: 26.02 Å2
Refinement stepCycle: final / Resolution: 2.476→41.071 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17186 0 2 94 17282
Biso mean--51.02 40.29 -
Num. residues----2148
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6142X-RAY DIFFRACTION8.543TORSIONAL
12C6142X-RAY DIFFRACTION8.543TORSIONAL
21B3820X-RAY DIFFRACTION8.543TORSIONAL
22D3820X-RAY DIFFRACTION8.543TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4761-2.5380.36271250.2784259848
2.538-2.60660.29622650.2703504795
2.6066-2.68330.33942750.2605507795
2.6833-2.76990.31062520.2501520897
2.7699-2.86890.32422640.2449518397
2.8689-2.98370.32842860.2455516897
2.9837-3.11950.29832980.2317518798
3.1195-3.28390.27782950.2194523798
3.2839-3.48950.29542480.2235521798
3.4895-3.75880.24142740.2006526198
3.7588-4.13670.23843180.1818516498
4.1367-4.73450.19192650.1615515997
4.7345-5.96210.23162750.167511096
5.9621-41.0710.18042320.1583508495
Refinement TLS params.Method: refined / Origin x: 43.888 Å / Origin y: 17.142 Å / Origin z: 17.411 Å
111213212223313233
T0.3549 Å2-0.0093 Å2-0.0887 Å2-0.2986 Å2-0.0674 Å2--0.326 Å2
L0.2617 °20.1472 °2-0.1997 °2-0.3311 °2-0.1769 °2--0.1885 °2
S-0.0053 Å °0.0273 Å °-0.037 Å °0.0672 Å °-0.0086 Å °-0.0437 Å °-0.0208 Å °-0.0367 Å °0.0111 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:694 OR RESID 801:801 OR RESID 901:935 ) ) OR ( CHAIN C AND ( RESID 6:700 OR RESID 801:801 OR RESID 901:917 ) ) OR ( CHAIN B AND ( RESID 3:416 OR RESID 501:531 ) ) OR ( CHAIN D AND ( RESID 3:413 OR RESID 501:511 ) )A4 - 694
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:694 OR RESID 801:801 OR RESID 901:935 ) ) OR ( CHAIN C AND ( RESID 6:700 OR RESID 801:801 OR RESID 901:917 ) ) OR ( CHAIN B AND ( RESID 3:416 OR RESID 501:531 ) ) OR ( CHAIN D AND ( RESID 3:413 OR RESID 501:511 ) )A801
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:694 OR RESID 801:801 OR RESID 901:935 ) ) OR ( CHAIN C AND ( RESID 6:700 OR RESID 801:801 OR RESID 901:917 ) ) OR ( CHAIN B AND ( RESID 3:416 OR RESID 501:531 ) ) OR ( CHAIN D AND ( RESID 3:413 OR RESID 501:511 ) )A901 - 935
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:694 OR RESID 801:801 OR RESID 901:935 ) ) OR ( CHAIN C AND ( RESID 6:700 OR RESID 801:801 OR RESID 901:917 ) ) OR ( CHAIN B AND ( RESID 3:416 OR RESID 501:531 ) ) OR ( CHAIN D AND ( RESID 3:413 OR RESID 501:511 ) )C6 - 700
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:694 OR RESID 801:801 OR RESID 901:935 ) ) OR ( CHAIN C AND ( RESID 6:700 OR RESID 801:801 OR RESID 901:917 ) ) OR ( CHAIN B AND ( RESID 3:416 OR RESID 501:531 ) ) OR ( CHAIN D AND ( RESID 3:413 OR RESID 501:511 ) )C801
6X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:694 OR RESID 801:801 OR RESID 901:935 ) ) OR ( CHAIN C AND ( RESID 6:700 OR RESID 801:801 OR RESID 901:917 ) ) OR ( CHAIN B AND ( RESID 3:416 OR RESID 501:531 ) ) OR ( CHAIN D AND ( RESID 3:413 OR RESID 501:511 ) )C901 - 917
7X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:694 OR RESID 801:801 OR RESID 901:935 ) ) OR ( CHAIN C AND ( RESID 6:700 OR RESID 801:801 OR RESID 901:917 ) ) OR ( CHAIN B AND ( RESID 3:416 OR RESID 501:531 ) ) OR ( CHAIN D AND ( RESID 3:413 OR RESID 501:511 ) )B3 - 416
8X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:694 OR RESID 801:801 OR RESID 901:935 ) ) OR ( CHAIN C AND ( RESID 6:700 OR RESID 801:801 OR RESID 901:917 ) ) OR ( CHAIN B AND ( RESID 3:416 OR RESID 501:531 ) ) OR ( CHAIN D AND ( RESID 3:413 OR RESID 501:511 ) )B501 - 531
9X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:694 OR RESID 801:801 OR RESID 901:935 ) ) OR ( CHAIN C AND ( RESID 6:700 OR RESID 801:801 OR RESID 901:917 ) ) OR ( CHAIN B AND ( RESID 3:416 OR RESID 501:531 ) ) OR ( CHAIN D AND ( RESID 3:413 OR RESID 501:511 ) )D3 - 413
10X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:694 OR RESID 801:801 OR RESID 901:935 ) ) OR ( CHAIN C AND ( RESID 6:700 OR RESID 801:801 OR RESID 901:917 ) ) OR ( CHAIN B AND ( RESID 3:416 OR RESID 501:531 ) ) OR ( CHAIN D AND ( RESID 3:413 OR RESID 501:511 ) )D501 - 511

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