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

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Basic information

Entry
Database: PDB / ID: 7esy
TitleCrystal structure of the complex formed by Wolbachia cytoplasmic incompatibility factors CidA and CidBND1-ND2 from wPip
Components
  • Bacteria factor 1
  • ULP_PROTEASE domain-containing protein
KeywordsPROTEIN BINDING / Wolbachia / deubiquitylase / antitoxin / cytoplasmic incompatibility
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_IV beta/2 protein / ULP_PROTEASE domain-containing protein
Function and homology information
Biological speciesWolbachia pipientis subsp. Culex pipiens
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.297 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 / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacteria factor 1
B: ULP_PROTEASE domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,3963
Polymers146,3562
Non-polymers401
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-8 kcal/mol
Surface area46420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.361, 154.556, 83.393
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Bacteria factor 1


Mass: 57482.438 Da / Num. of mol.: 1
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: Protein ULP_PROTEASE domain-containing protein


Mass: 88873.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wolbachia pipientis subsp. Culex pipiens (strain wPip) (bacteria)
Strain: wPip / Gene: WP0283 / Production host: Escherichia coli (E. coli) / References: UniProt: B3CP63
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.29 Å3/Da / Density % sol: 46.33 %
Crystal growTemperature: 289 K / Method: batch mode
Details: 0.2M calcium chloride dehydrate, pH 5.1, 20% w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97909 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97909 Å / Relative weight: 1
ReflectionResolution: 2.297→50 Å / Num. obs: 59653 / % possible obs: 96.54 % / Redundancy: 12.8 % / Biso Wilson estimate: 46.43 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 16.6
Reflection shellResolution: 2.297→2.379 Å / Redundancy: 10 % / Rmerge(I) obs: 1.729 / Num. unique obs: 5741 / % possible all: 87.08

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
PHENIXmodel building
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.297→49.587 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 28.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2433 1914 3.32 %
Rwork0.2169 55783 -
obs0.2178 57697 96.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.78 Å2 / Biso mean: 59.7603 Å2 / Biso min: 34.58 Å2
Refinement stepCycle: final / Resolution: 2.297→49.587 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9142 0 1 55 9198
Biso mean--60.66 51.43 -
Num. residues----1138
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2972-2.37930.34211700.3464497487
2.3793-2.47450.34281720.31525992
2.4745-2.58710.3341830.284538195
2.5871-2.72350.33631870.2723550896
2.7235-2.89420.27521940.2479557098
2.8942-3.11760.26521960.2346569199
3.1176-3.43120.27051980.2371570999
3.4312-3.92760.24022000.20395788100
3.9276-4.94760.19982030.17645842100
4.9476-49.5870.20872110.1946061100
Refinement TLS params.Method: refined / Origin x: 72.992 Å / Origin y: 39.153 Å / Origin z: 82.689 Å
111213212223313233
T0.4582 Å20.025 Å20.0167 Å2-0.4233 Å20.0178 Å2--0.3819 Å2
L0.3403 °20.1637 °20.174 °2-0.5532 °20.3071 °2--0.6657 °2
S0.0338 Å °0.0097 Å °-0.0136 Å °0.0387 Å °0.0017 Å °0.0141 Å °0.0775 Å °0.0678 Å °-0.0344 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:428 OR RESID 1301:1316 ) ) OR ( CHAIN B AND ( RESID 1201:1201 OR RESID 1301:1339 OR RESID 5:757 ) )A2 - 428
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:428 OR RESID 1301:1316 ) ) OR ( CHAIN B AND ( RESID 1201:1201 OR RESID 1301:1339 OR RESID 5:757 ) )A1301 - 1316
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:428 OR RESID 1301:1316 ) ) OR ( CHAIN B AND ( RESID 1201:1201 OR RESID 1301:1339 OR RESID 5:757 ) )B1201
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:428 OR RESID 1301:1316 ) ) OR ( CHAIN B AND ( RESID 1201:1201 OR RESID 1301:1339 OR RESID 5:757 ) )B1301 - 1339
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:428 OR RESID 1301:1316 ) ) OR ( CHAIN B AND ( RESID 1201:1201 OR RESID 1301:1339 OR RESID 5:757 ) )B5 - 757

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