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- PDB-8htc: Crystal structure of a SeMet-labeled effector from Chromobacteriu... -

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Basic information

Entry
Database: PDB / ID: 8htc
TitleCrystal structure of a SeMet-labeled effector from Chromobacterium violaceum in complex with Ubiquitin
Components
  • NAD(+)--protein-threonine ADP-ribosyltransferase
  • Ubiquitin-40S ribosomal protein S27a (Fragment)
KeywordsTRANSFERASE / Ubiquitination
Function / homology
Function and homology information


glycosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / host cell / extracellular region
Similarity search - Function
S27a-like superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Ubiquitin-ribosomal protein eS31 fusion protein / NAD(+)--protein-threonine ADP-ribosyltransferase
Similarity search - Component
Biological speciesChromobacterium violaceum ATCC 12472 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsTan, J. / Wang, X. / Zhou, Y. / Zhu, Y.
Funding support China, 6items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81530068 China
National Natural Science Foundation of China (NSFC)81322024 China
National Natural Science Foundation of China (NSFC)31370722 China
National Natural Science Foundation of China (NSFC)81561130162 China
National Natural Science Foundation of China (NSFC)81501717 China
Ministry of Science and Technology (MoST, China)2017YFA0503900 China
CitationJournal: Nat.Chem.Biol. / Year: 2024
Title: Molecular basis of threonine ADP-ribosylation of ubiquitin by bacterial ARTs.
Authors: Tan, J. / Xu, Y. / Wang, X. / Yan, F. / Xian, W. / Liu, X. / Chen, Y. / Zhu, Y. / Zhou, Y.
History
DepositionDec 21, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD(+)--protein-threonine ADP-ribosyltransferase
B: Ubiquitin-40S ribosomal protein S27a (Fragment)


Theoretical massNumber of molelcules
Total (without water)35,3952
Polymers35,3952
Non-polymers00
Water1,946108
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.490, 74.460, 50.460
Angle α, β, γ (deg.)90.000, 99.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NAD(+)--protein-threonine ADP-ribosyltransferase / Adenosine diphosphate-ribosyltransferase / ADP-ribosyltransferase / Type III effector CteC


Mass: 26407.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum ATCC 12472 (bacteria)
Strain: ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757
Gene: cteC, CV_1467 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: Q7NY09, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Protein Ubiquitin-40S ribosomal protein S27a (Fragment)


Mass: 8988.284 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS27A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: J3QTR3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.05 Å3/Da / Density % sol: 39.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.25
Details: 100 mM sodium cacodylate, pH 6.25, 200 mM sodium acetate, 22% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.2→41.409 Å / Num. obs: 27318 / % possible obs: 97.3 % / Redundancy: 2.738 % / Biso Wilson estimate: 40.397 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.109 / Rrim(I) all: 0.134 / Χ2: 1.081 / Net I/σ(I): 6.21 / Num. measured all: 74784
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.2-2.262.4760.382.34474209718070.7730.47586.2
2.26-2.322.740.3452.785434199819830.8340.42199.2
2.32-2.392.8050.313.15493196119580.890.37899.8
2.39-2.462.8310.263.635354190218910.9060.31899.4
2.46-2.542.8150.2274.145273187618730.9320.27799.8
2.54-2.632.8080.214.564951179217630.9320.25798.4
2.63-2.732.7590.1875.124712171917080.9440.22999.4
2.73-2.842.6810.1685.494292165216010.9450.20796.9
2.84-2.972.6450.1476.34181165515810.960.18295.5
2.97-3.112.8650.1277.394231148714770.9730.15599.3
3.11-3.282.8320.128.284035143914250.9680.14699
3.28-3.482.7610.1068.773771138413660.9740.1398.7
3.48-3.722.7410.1039.393426128212500.9740.12597.5
3.72-4.022.6470.0869.623084119711650.9830.10697.3
4.02-4.42.5670.0859.742608110610160.9770.10691.9
4.4-4.922.8470.0810.582864101410060.9850.09899.2
4.92-5.682.7910.08910.5224428848750.9720.10999
5.68-6.962.6720.09110.0219377347250.9780.11298.8
6.96-9.842.5940.07510.5514145775450.9890.09394.5
9.84-41.4092.6670.07211.268083113030.9890.08997.4

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.14_3228refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→41.409 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 26.02
RfactorNum. reflection% reflection
Rfree0.2468 1359 4.98 %
Rwork0.1919 --
obs0.1945 27314 97.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.32 Å2 / Biso mean: 42.6331 Å2 / Biso min: 12.42 Å2
Refinement stepCycle: final / Resolution: 2.2→41.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2308 0 0 108 2416
Biso mean---42.74 -
Num. residues----297
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2004-2.27910.33531230.2711238289
2.2791-2.37030.29181370.25522637100
2.3703-2.47820.31831380.25082657100
2.4782-2.60880.33861390.2544264599
2.6088-2.77230.3381420.2331264599
2.7723-2.98620.30511360.2267258896
2.9862-3.28660.21561340.1991260299
3.2866-3.7620.23741420.1736262998
3.762-4.73860.2141320.1417254896
4.7386-41.4090.18091360.1618262298
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)
11.36580.80540.57721.29390.62630.7671-0.0962-0.1704-0.2118-0.1583-0.0885-0.0859-0.124-0.0638-0.23940.18840.02820.04550.15390.02370.21417.3156.920817.666
20.07610.08860.10750.12330.00420.10860.14030.1477-0.0159-0.3415-0.1773-0.06830.12170.18870.00030.21310.07980.02630.23530.00040.229524.017112.873515.6751
30.4497-0.09960.29080.0289-0.00160.3902-0.1488-0.0093-0.03690.03530.0220.18060.32820.7881-0.01170.2920.0738-0.02220.2778-0.00750.203235.961227.9056.0721
40.53840.4046-0.48390.2734-0.32440.3839-0.0171-0.17110.0023-0.4021-0.1790.0532-0.06740.0401-0.18110.2870.0393-0.05350.1903-0.01730.213322.14623.896115.529
51.0660.6230.48711.48150.61280.6973-0.0131-0.78160.0483-0.7752-0.3551-0.0342-0.0064-0.6677-0.46610.05030.09860.00310.17040.0140.16027.98083.768816.6379
60.03840.0150.0061-0.01130.02550.0996-0.2119-0.0947-0.16260.1261-0.1327-0.11180.53340.37780.00040.58980.19760.06160.40360.02490.344832.568214.8321-11.9472
70.0810.2183-0.08980.6518-0.26710.1455-0.18470.30880.0133-0.63420.31150.25210.71810.6928-0.0420.13210.1834-0.0020.4633-0.05150.154838.780322.5384-14.94
80.18940.00720.09190.1084-0.03920.0588-0.06190.3131-0.442-0.15830.0346-0.49350.25140.13420.01760.35280.23060.0990.6442-0.01970.287641.535218.1202-3.557
90.50110.048-0.06380.18580.17430.2248-0.3332-0.3470.33090.08960.0636-0.03281.06220.6671-0.19340.4890.2170.0280.48520.0718-0.032136.865618.7817-6.238
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 44 through 116 )A44 - 116
2X-RAY DIFFRACTION2chain 'A' and (resid 117 through 150 )A117 - 150
3X-RAY DIFFRACTION3chain 'A' and (resid 151 through 187 )A151 - 187
4X-RAY DIFFRACTION4chain 'A' and (resid 188 through 226 )A188 - 226
5X-RAY DIFFRACTION5chain 'A' and (resid 227 through 276 )A227 - 276
6X-RAY DIFFRACTION6chain 'B' and (resid -2 through 22 )B-2 - 22
7X-RAY DIFFRACTION7chain 'B' and (resid 23 through 44 )B23 - 44
8X-RAY DIFFRACTION8chain 'B' and (resid 45 through 56 )B45 - 56
9X-RAY DIFFRACTION9chain 'B' and (resid 57 through 75 )B57 - 75

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