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- PDB-6yhm: Crystal structure of the C-terminal domain of CNFy from Yersinia ... -

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Basic information

Entry
Database: PDB / ID: 6yhm
TitleCrystal structure of the C-terminal domain of CNFy from Yersinia pseudotuberculosis
ComponentsCytotoxic necrotizing factor
KeywordsTOXIN / CNF / cytotoxic necrotizing factor / deamidase / RhoA modification / RhoA activation / putative ADP-ribosyltransferase
Function / homologyCytotoxic 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 / Cytotoxic necrotizing factor
Function and homology information
Biological speciesYersinia pseudotuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.13 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
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytotoxic necrotizing factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8682
Polymers32,8431
Non-polymers241
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-9 kcal/mol
Surface area12790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.981, 50.160, 69.728
Angle α, β, γ (deg.)90.000, 98.720, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein Cytotoxic necrotizing factor


Mass: 32843.496 Da / Num. of mol.: 1 / Fragment: C-terminal Catalytic Domain, residues 719 - 1014
Source method: isolated from a genetically manipulated source
Details: C-terminal domain of CNFy from Yersinia pseudotuberculosis (residues 720-1014) Residues 716-719 are overhangs from digestion of the expression tag.
Source: (gene. exp.) Yersinia pseudotuberculosis (bacteria) / Gene: cnf / Plasmid: pET28c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0N9JNY6
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.24 Å3/Da / Density % sol: 45.06 % / Mosaicity: 0.24 °
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.2 M ammonium fluoride, 20 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.13→68.92 Å / Num. obs: 100708 / % possible obs: 95.3 % / Redundancy: 3 % / Biso Wilson estimate: 12.24 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.024 / Rrim(I) all: 0.043 / Net I/σ(I): 16 / Num. measured all: 303327
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.13-1.22.90.405153270.8850.2720.4999.7
3.59-68.922.70.02124640.9980.0150.02671.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.18rc4_3812refinement
PHENIX1.18rc4_3812refinement
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HQ0

1hq0


Resolution: 1.13→31.97 Å / SU ML: 0.1036 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.4796
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1852 5090 5.06 %
Rwork0.1674 95553 -
obs0.1683 100643 95.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.92 Å2
Refinement stepCycle: LAST / Resolution: 1.13→31.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2271 0 1 340 2612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00652481
X-RAY DIFFRACTIONf_angle_d0.92783395
X-RAY DIFFRACTIONf_chiral_restr0.0804391
X-RAY DIFFRACTIONf_plane_restr0.0057445
X-RAY DIFFRACTIONf_dihedral_angle_d15.0783936
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.13-1.150.25471840.25573334X-RAY DIFFRACTION99.66
1.15-1.160.27031650.23963281X-RAY DIFFRACTION99.6
1.16-1.180.26911520.24453331X-RAY DIFFRACTION99.54
1.18-1.190.25551820.23693335X-RAY DIFFRACTION99.52
1.19-1.210.23371770.23113336X-RAY DIFFRACTION100
1.21-1.220.24631860.22063322X-RAY DIFFRACTION99.83
1.22-1.240.22721660.21583285X-RAY DIFFRACTION99.6
1.24-1.260.21622020.21513332X-RAY DIFFRACTION99.72
1.26-1.280.20921710.20743315X-RAY DIFFRACTION99.46
1.28-1.30.22611780.1983305X-RAY DIFFRACTION99.6
1.3-1.320.24461900.19633313X-RAY DIFFRACTION99.66
1.32-1.350.19221760.19363315X-RAY DIFFRACTION99.83
1.35-1.370.1771910.18993302X-RAY DIFFRACTION99.69
1.37-1.40.21461570.18753412X-RAY DIFFRACTION99.72
1.4-1.430.19221800.18533310X-RAY DIFFRACTION99.71
1.43-1.460.19691830.18233304X-RAY DIFFRACTION99.69
1.46-1.50.20491790.17233309X-RAY DIFFRACTION99.37
1.5-1.540.18171150.16872274X-RAY DIFFRACTION67.83
1.54-1.590.18751950.16133275X-RAY DIFFRACTION99.26
1.59-1.640.17031700.15443328X-RAY DIFFRACTION99.09
1.64-1.70.1461700.15043349X-RAY DIFFRACTION99.15
1.7-1.760.15511620.15283309X-RAY DIFFRACTION98.86
1.76-1.840.18021720.15553324X-RAY DIFFRACTION98.73
1.84-1.940.18621430.15592423X-RAY DIFFRACTION72.53
1.94-2.060.15421640.15073300X-RAY DIFFRACTION98.55
2.06-2.220.15051670.14832942X-RAY DIFFRACTION87.5
2.22-2.440.17371440.15072849X-RAY DIFFRACTION84.24
2.44-2.80.1831650.14743087X-RAY DIFFRACTION91.22
2.8-3.520.17631570.15483167X-RAY DIFFRACTION93.71
3.52-31.970.19441470.17322485X-RAY DIFFRACTION72.03
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)
10.70370541238-0.07372361507690.4518530783452.233647190850.8669829305742.42960076957-0.06268579522480.1096980682850.00787896331337-0.184239421921-0.04048605363140.2632572669830.0195150717384-0.1935696486830.06129425436080.07700154759530.00177840649236-0.03252834810380.136659226425-0.01207765155230.12032136554835.6748234974.490403495853.55380862951
20.639788031689-0.1002374006280.2193613673851.532208604130.9113797413072.216839887320.0282816038572-0.0799448173195-0.07688714158570.4113431981260.02846276940660.04326160731960.464200523023-0.104582578975-0.08345845054470.2754941532470.01540413690690.05215187457050.1034931215060.02918280217740.15027048644843.0353620697-3.8088705573927.3480394568
31.22882733849-0.7618542710030.1418125445831.479363358620.3622816897521.78056714765-0.05662289172990.0786218344458-0.0697450813607-0.324185775327-0.04266006254640.1829820981080.304341985035-0.3388068058970.06040792147660.26905913701-0.04558637444570.06550082519850.1338442830260.01486761731110.18892009021534.4135107503-2.6365187395327.7543846047
40.5915506061870.1238114125330.6106147628450.791557379960.2821481065991.90911257781-0.009344361364050.0327414126737-0.02140666160140.0854820546485-0.02899938087750.1619901682690.163210958624-0.1376363262180.0421577120480.103722452656-0.006852874763960.02043453674740.0990333805965-0.006026410802010.11982098983738.10018624111.0442656222313.7153495587
51.026976910820.0458288904516-0.2176276414111.60661663280.3038528363331.51225282029-0.0466407331661-0.1059621894490.005380749934210.2974284499940.0286698113361-0.04581073331440.1557136940630.2357327544150.01530713217450.1459821410190.0374774121962-0.003766476585980.1220975657070.0006066677813560.093127360621750.84480108397.3927935380826.8221234383
61.04407593014-0.275228282209-0.06795061529631.108994721220.1161126083761.309154221-0.0470925972181-0.0870750040460.09495209100350.1178020539590.0835561182655-0.162018403817-0.09540559288380.335075295706-0.02960433376860.112896771566-0.000937992811136-0.01984600842580.160411575465-0.009336656300620.12256731565957.171382198715.193687530322.8980429179
71.676752362590.2065117329060.1640740811471.614550742570.06211856476531.87158927593-0.0178740565160.1227013389480.130128931567-0.029729394347-0.01777982204150.0455129849309-0.146826916551-0.02375059843880.02643519191890.08430091725180.0100062776431-0.01101642233250.1188387863470.01966109536580.085070353799445.615755269513.715120926811.2183037361
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 719 through 750 )719 - 7501 - 45
22chain 'A' and (resid 751 through 774 )751 - 77448 - 72
33chain 'A' and (resid 775 through 799 )775 - 79973 - 103
44chain 'A' and (resid 800 through 859 )800 - 859104 - 171
55chain 'A' and (resid 860 through 920 )860 - 920172 - 244
66chain 'A' and (resid 921 through 956 )921 - 956245 - 289
77chain 'A' and (resid 957 through 1014 )957 - 1014290 - 354

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