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- PDB-6yhn: Crystal structure of domains 4-5 of CNFy from Yersinia pseudotube... -

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Basic information

Entry
Database: PDB / ID: 6yhn
TitleCrystal structure of domains 4-5 of CNFy from Yersinia pseudotuberculosis
ComponentsCytotoxic necrotizing factor
KeywordsTOXIN / CNF / cytotoxic necrotizing factor / deamidase / RhoA modification / RhoA activation / putative ADP-ribosyltransferase
Function / homology
Function and homology information


Cytotoxic necrotizing factor, Rho-activating domain / Domain of unknown function DUF4765 / Cytotoxic necrotizing factor, Rho-activating domain superfamily / Rho-activating domain of cytotoxic necrotizing factor / Domain of unknown function (DUF4765) / Domain of unknown function DUF6543 / Family of unknown function (DUF6543) / Cytotoxic necrotizing factor-like, catalytic
Similarity search - Domain/homology
(R,R)-2,3-BUTANEDIOL / Cytotoxic necrotizing factor
Similarity search - Component
Biological speciesYersinia pseudotuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
Model detailsStructure comprises residues 1-1014, active site cysteine 866 has been mutated to serine
AuthorsLukat, P. / Gazdag, E.M. / Heidler, T.V. / Blankenfeldt, W.
CitationJournal: Embo J. / Year: 2021
Title: Crystal structure of bacterial cytotoxic necrotizing factor CNF Y reveals molecular building blocks for intoxication.
Authors: Chaoprasid, P. / Lukat, P. / Muhlen, S. / Heidler, T. / Gazdag, E.M. / Dong, S. / Bi, W. / Ruter, C. / Kirchenwitz, M. / Steffen, A. / Jansch, L. / Stradal, T.E.B. / Dersch, P. / Blankenfeldt, W.
History
DepositionMar 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 24, 2021Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytotoxic necrotizing factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,21410
Polymers57,8491
Non-polymers3659
Water6,612367
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-66 kcal/mol
Surface area20070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.271, 90.531, 120.717
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cytotoxic necrotizing factor


Mass: 57848.938 Da / Num. of mol.: 1 / Fragment: CNFy residues 526-1014
Source method: isolated from a genetically manipulated source
Details: Fragment of CNFy comprising residues 526-1014. Cys 866 has found to be oxidized in the structure.
Source: (gene. exp.) Yersinia pseudotuberculosis (bacteria) / Gene: cnf / Plasmid: pCOLA-Duet-1
Details (production host): pCOLA-Duet-1 has been modified with sequence encoding for N-terminal Strep-tag II and TEV protease cleavage site and C-terminal 3 x FLAG epitope
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0N9JNY6

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Non-polymers , 6 types, 376 molecules

#2: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 367 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.19 Å3/Da / Density % sol: 43.88 % / Mosaicity: 0.1 °
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.24 M magnesium chloride, 22.5 % (w/v) PEG 2000 MME, 1 mM ATP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→48.27 Å / Num. obs: 49960 / % possible obs: 99.9 % / Redundancy: 32.7 % / CC1/2: 0.982 / Rmerge(I) obs: 0.257 / Rpim(I) all: 0.046 / Rrim(I) all: 0.261 / Net I/σ(I): 12.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.8-1.8419.83.5628850.8160.8153.65398.6
9-48.2729.90.0654880.9990.0120.06799.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.6.3data scaling
PHASERphasing
PHENIX1.14rc1_3177refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Corresponding fragment from the full-length toxin

Resolution: 1.8→45.265 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.23
RfactorNum. reflection% reflection
Rfree0.191 2410 4.84 %
Rwork0.1581 --
obs0.1598 49821 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 150.78 Å2 / Biso mean: 38.201 Å2 / Biso min: 12.4 Å2
Refinement stepCycle: final / Resolution: 1.8→45.265 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3602 0 28 367 3997
Biso mean--71.45 42.28 -
Num. residues----460
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.8-1.83680.35461370.30342740
1.8368-1.87670.31531440.2552696
1.8767-1.92040.25441310.2242783
1.9204-1.96840.18481170.1892786
1.9684-2.02160.19351330.17252733
2.0216-2.08110.19241360.16972766
2.0811-2.14830.19861370.16152769
2.1483-2.2250.2221390.15612767
2.225-2.31410.17851380.14962773
2.3141-2.41940.19131600.14992757
2.4194-2.5470.18681300.15552795
2.547-2.70650.20711620.15242761
2.7065-2.91550.22121310.16382791
2.9155-3.20880.18871650.15862809
3.2088-3.67290.15921480.13632835
3.6729-4.62680.14811480.12432843
4.6268-45.2650.20041540.16663007
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)
10.7809-0.20940.37741.0179-0.25060.84440.04950.1619-0.1493-0.0932-0.1535-0.09150.43870.61430.00450.28860.05090.03860.30530.03150.2648-4.9551-8.89517.439
21.0334-0.7952-0.28781.433-0.48050.9754-0.12030.109-0.2610.0965-0.01680.2840.1688-0.4688-0.00710.2213-0.0590.04630.3359-0.03290.2526-23.4596-4.704212.6971
30.5852-0.45840.42660.7708-0.41210.3399-0.0782-0.14640.11710.08820.00780.1087-0.2934-0.20610.00170.23340.0150.01340.318-0.01620.2248-19.74672.52713.6959
40.09230.10430.01870.4987-0.56152.13890.02240.004-0.11590.0396-0.08760.02290.14440.0532-0.00660.19610.00830.00870.2493-0.0110.2074-14.2059-1.46234.02
51.6713-0.36690.33021.45880.3023.425-0.0259-0.13830.07680.0271-0.04190.0887-0.13910.0342-0.01980.1507-0.0153-0.00560.1236-0.03010.179-18.115711.6676-11.5869
62.3835-0.89490.03472.58-0.02893.4672-0.08280.09310.1975-0.2333-0.09130.1943-0.5613-0.1243-0.11690.28130.0108-0.05820.1487-0.00810.209-21.240917.3919-25.574
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 524 through 562 )A524 - 562
2X-RAY DIFFRACTION2chain 'A' and (resid 563 through 621 )A563 - 621
3X-RAY DIFFRACTION3chain 'A' and (resid 622 through 654 )A622 - 654
4X-RAY DIFFRACTION4chain 'A' and (resid 655 through 733 )A655 - 733
5X-RAY DIFFRACTION5chain 'A' and (resid 734 through 908 )A734 - 908
6X-RAY DIFFRACTION6chain 'A' and (resid 909 through 1016 )A909 - 1016

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