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- PDB-7et0: Crystal structure of the complex formed by Wolbachia cytoplasmic ... -

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Basic information

Entry
Database: PDB / ID: 7et0
TitleCrystal structure of the complex formed by Wolbachia cytoplasmic incompatibility factors CinA and CinB from wPip
Components
  • Bacteria factor A
  • Bacteria factor B
KeywordsPROTEIN BINDING / Wolbachia / Nuclease / Antitoxin / Toxin
Function / homologyUncharacterized protein / ANK_REP_REGION domain-containing protein
Function and homology information
Biological speciesWolbachia pipientis subsp. Culex pipiens
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 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


Theoretical massNumber of molelcules
Total (without water)273,8564
Polymers273,8564
Non-polymers00
Water2,270126
1
A: Bacteria factor B
B: Bacteria factor A


Theoretical massNumber of molelcules
Total (without water)136,9282
Polymers136,9282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-2 kcal/mol
Surface area42950 Å2
MethodPISA
2
C: Bacteria factor B
D: Bacteria factor A


Theoretical massNumber of molelcules
Total (without water)136,9282
Polymers136,9282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint0 kcal/mol
Surface area43510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.805, 87.118, 92.215
Angle α, β, γ (deg.)111.270, 90.970, 114.670
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 6 through 16 or (resid 17...
21(chain C and (resid 6 through 28 or (resid 29...
12(chain B and (resid 3 through 110 or (resid 111...
22(chain D and ((resid 3 and (name N or name...

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
111LYSLYSMETMET(chain A and (resid 6 through 16 or (resid 17...AA6 - 166 - 16
121ARGARGARGARG(chain A and (resid 6 through 16 or (resid 17...AA1717
131ASNASNASNASN(chain A and (resid 6 through 16 or (resid 17...AA4 - 6944 - 694
141ASNASNASNASN(chain A and (resid 6 through 16 or (resid 17...AA4 - 6944 - 694
151ASNASNASNASN(chain A and (resid 6 through 16 or (resid 17...AA4 - 6944 - 694
161ASNASNASNASN(chain A and (resid 6 through 16 or (resid 17...AA4 - 6944 - 694
211LYSLYSGLNGLN(chain C and (resid 6 through 28 or (resid 29...CC6 - 286 - 28
221LYSLYSLYSLYS(chain C and (resid 6 through 28 or (resid 29...CC2929
231LYSLYSASPASP(chain C and (resid 6 through 28 or (resid 29...CC6 - 7006 - 700
241LYSLYSASPASP(chain C and (resid 6 through 28 or (resid 29...CC6 - 7006 - 700
251LYSLYSASPASP(chain C and (resid 6 through 28 or (resid 29...CC6 - 7006 - 700
261LYSLYSASPASP(chain C and (resid 6 through 28 or (resid 29...CC6 - 7006 - 700
112SERSERASPASP(chain B and (resid 3 through 110 or (resid 111...BB3 - 1103 - 110
122LYSLYSLYSLYS(chain B and (resid 3 through 110 or (resid 111...BB111111
132GLUGLUILEILE(chain B and (resid 3 through 110 or (resid 111...BB2 - 4162 - 416
142GLUGLUILEILE(chain B and (resid 3 through 110 or (resid 111...BB2 - 4162 - 416
152GLUGLUILEILE(chain B and (resid 3 through 110 or (resid 111...BB2 - 4162 - 416
162GLUGLUILEILE(chain B and (resid 3 through 110 or (resid 111...BB2 - 4162 - 416
212SERSERSERSER(chain D and ((resid 3 and (name N or name...DD33
222SERSERSERSER(chain D and ((resid 3 and (name N or name...DD3 - 4153 - 415
232SERSERSERSER(chain D and ((resid 3 and (name N or name...DD3 - 4153 - 415
242SERSERSERSER(chain D and ((resid 3 and (name N or name...DD3 - 4153 - 415
252SERSERSERSER(chain D and ((resid 3 and (name N or name...DD3 - 4153 - 415

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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.12 Å3/Da / Density % sol: 42.04 %
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: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.194→50 Å / Num. obs: 109042 / % possible obs: 97.2 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.043 / Rrim(I) all: 0.126 / Χ2: 1.668 / Net I/σ(I): 25.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.246.31.38153170.8240.5681.4990.595
2.24-2.286.61.13253030.2390.4691.230.72594.9
2.28-2.327.10.97552790.7440.3821.050.45194.1
2.32-2.378.20.83754750.8440.3050.8920.45897.4
2.37-2.428.60.7454280.8940.2640.7870.47597.5
2.42-2.488.70.6254850.9170.2190.6590.48297.5
2.48-2.548.70.53454540.9230.1890.5670.50197.4
2.54-2.618.70.43254790.9560.1530.4590.53197.5
2.61-2.698.60.37354590.9580.1340.3970.60397.3
2.69-2.778.30.28354430.9740.1030.3020.62896.7
2.77-2.878.30.23253170.9790.0850.2470.69395.5
2.87-2.9990.19155390.9870.0670.2030.77198.3
2.99-3.1290.15855010.9890.0550.1680.89898.3
3.12-3.298.90.12855280.9920.0450.1361.12398.3
3.29-3.498.80.11454800.9920.040.1211.42697.7
3.49-3.768.20.154310.9930.0370.1061.79296.9
3.76-4.149.10.0955420.9950.0310.0952.07599
4.14-4.7490.08555440.9950.030.0912.81698.9
4.74-5.978.50.09154750.9910.0330.0974.14297.7
5.97-508.70.10555630.9580.0390.11211.00498.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
PHENIXmodel building
AutoSolphasing
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.2→46.328 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0.14 / Phase error: 31.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2485 1946 1.84 %
Rwork0.219 103724 -
obs0.2195 105670 93.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.21 Å2 / Biso mean: 62.1013 Å2 / Biso min: 29.58 Å2
Refinement stepCycle: final / Resolution: 2.2→46.328 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16981 0 0 126 17107
Biso mean---50.52 -
Num. residues----2158
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6013X-RAY DIFFRACTION8.369TORSIONAL
12C6013X-RAY DIFFRACTION8.369TORSIONAL
21B3596X-RAY DIFFRACTION8.369TORSIONAL
22D3596X-RAY DIFFRACTION8.369TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.23930.3809800.359440767
2.2393-2.2880.37431210.3544539984
2.288-2.34120.3338940.3003586189
2.3412-2.39970.27881090.2726601492
2.3997-2.46460.28681240.2676605893
2.4646-2.53710.34381140.2707615994
2.5371-2.6190.30011070.2656623995
2.619-2.71260.27391180.2664620895
2.7126-2.82120.33311250.27611393
2.8212-2.94960.34941150.2626636797
2.9496-3.10510.32241150.267642498
3.1051-3.29960.30591230.2454640498
3.2996-3.55420.29621140.2356636698
3.5542-3.91170.21821230.2073639597
3.9117-4.47740.22261240.182644899
4.4774-5.63940.20421210.1766639998
5.6394-46.3280.17531190.1828646399
Refinement TLS params.Method: refined / Origin x: 43.63 Å / Origin y: 16.866 Å / Origin z: 17.758 Å
111213212223313233
T0.3839 Å20.0301 Å2-0.0403 Å2-0.2943 Å2-0.0529 Å2--0.3534 Å2
L0.5999 °20.1592 °2-0.2436 °2-0.2984 °2-0.1779 °2--0.2966 °2
S-0.0416 Å °0.0415 Å °-0.0116 Å °0.0808 Å °0.0267 Å °-0.0407 Å °0.0322 Å °-0.0361 Å °0.0123 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:694 OR RESID 801:851 ) ) OR ( CHAIN C AND ( RESID 6:700 OR RESID 801:822 ) ) OR ( CHAIN B AND ( RESID 2:416 OR RESID 501:543 ) ) OR ( CHAIN D AND ( RESID 501:510 OR RESID 3:415 ) )A4 - 694
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:694 OR RESID 801:851 ) ) OR ( CHAIN C AND ( RESID 6:700 OR RESID 801:822 ) ) OR ( CHAIN B AND ( RESID 2:416 OR RESID 501:543 ) ) OR ( CHAIN D AND ( RESID 501:510 OR RESID 3:415 ) )A801 - 851
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:694 OR RESID 801:851 ) ) OR ( CHAIN C AND ( RESID 6:700 OR RESID 801:822 ) ) OR ( CHAIN B AND ( RESID 2:416 OR RESID 501:543 ) ) OR ( CHAIN D AND ( RESID 501:510 OR RESID 3:415 ) )C6 - 700
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:694 OR RESID 801:851 ) ) OR ( CHAIN C AND ( RESID 6:700 OR RESID 801:822 ) ) OR ( CHAIN B AND ( RESID 2:416 OR RESID 501:543 ) ) OR ( CHAIN D AND ( RESID 501:510 OR RESID 3:415 ) )C801 - 822
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:694 OR RESID 801:851 ) ) OR ( CHAIN C AND ( RESID 6:700 OR RESID 801:822 ) ) OR ( CHAIN B AND ( RESID 2:416 OR RESID 501:543 ) ) OR ( CHAIN D AND ( RESID 501:510 OR RESID 3:415 ) )B2 - 416
6X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:694 OR RESID 801:851 ) ) OR ( CHAIN C AND ( RESID 6:700 OR RESID 801:822 ) ) OR ( CHAIN B AND ( RESID 2:416 OR RESID 501:543 ) ) OR ( CHAIN D AND ( RESID 501:510 OR RESID 3:415 ) )B501 - 543
7X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:694 OR RESID 801:851 ) ) OR ( CHAIN C AND ( RESID 6:700 OR RESID 801:822 ) ) OR ( CHAIN B AND ( RESID 2:416 OR RESID 501:543 ) ) OR ( CHAIN D AND ( RESID 501:510 OR RESID 3:415 ) )D501 - 510
8X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:694 OR RESID 801:851 ) ) OR ( CHAIN C AND ( RESID 6:700 OR RESID 801:822 ) ) OR ( CHAIN B AND ( RESID 2:416 OR RESID 501:543 ) ) OR ( CHAIN D AND ( RESID 501:510 OR RESID 3:415 ) )D3 - 415

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