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- PDB-8oi3: Structure of NopD with AtSUMO2 -

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Basic information

Entry
Database: PDB / ID: 8oi3
TitleStructure of NopD with AtSUMO2
Components
  • Small ubiquitin-related modifier 2
  • Type III effector
KeywordsHYDROLASE / SUMO protease / Complex / Plant SUMO2
Function / homology
Function and homology information


deNEDDylase activity / ubiquitin-like protein ligase binding / protein sumoylation / cysteine-type peptidase activity / protein tag activity / proteolysis / nucleus / cytoplasm
Similarity search - Function
NEDD8-specific protease 1/2-like / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Ulp1 protease family, C-terminal catalytic domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Papain-like cysteine peptidase superfamily / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
prop-2-en-1-amine / Type III effector / Small ubiquitin-related modifier 2
Similarity search - Component
Biological speciesBradyrhizobium (bacteria)
Arabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsReverter, D. / Li, Y.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and Universities Spain
CitationJournal: To Be Published
Title: Structure of NopD with AtSUMO2
Authors: Reverter, D. / Li, Y.
History
DepositionMar 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type III effector
B: Type III effector
C: Small ubiquitin-related modifier 2
D: Small ubiquitin-related modifier 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9746
Polymers67,8604
Non-polymers1142
Water5,495305
1
A: Type III effector
D: Small ubiquitin-related modifier 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9873
Polymers33,9302
Non-polymers571
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-3 kcal/mol
Surface area12200 Å2
2
B: Type III effector
C: Small ubiquitin-related modifier 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9873
Polymers33,9302
Non-polymers571
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-4 kcal/mol
Surface area12140 Å2
Unit cell
Length a, b, c (Å)80.851, 86.826, 90.485
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Type III effector


Mass: 23497.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium (bacteria) / Gene: nopD / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2U9K2V6
#2: Protein Small ubiquitin-related modifier 2 / AtSUMO2


Mass: 10432.643 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SUMO2, SUM2, At5g55160, MCO15.11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FLP6
#3: Chemical ChemComp-AYE / prop-2-en-1-amine / ALLYLAMINE


Mass: 57.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7N / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.34 Å3/Da / Density % sol: 47.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M Imidazole 7.0, 50% v/v MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.499→49.522 Å / Num. obs: 76890 / % possible obs: 92.6 % / Redundancy: 6.1 % / CC1/2: 0.999 / Net I/σ(I): 13.8
Reflection shellResolution: 1.499→1.634 Å / Num. unique obs: 3844 / CC1/2: 0.497

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: alphafold model

Resolution: 1.5→49.52 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2042 3911 5.09 %
Rwork0.1784 72964 -
obs0.1797 76875 74.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.01 Å2 / Biso mean: 33.9565 Å2 / Biso min: 11.26 Å2
Refinement stepCycle: final / Resolution: 1.5→49.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4184 0 22 305 4511
Biso mean--20.41 38.35 -
Num. residues----520
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.520.3649120.29891271394
1.52-1.540.3384110.3282102216
1.54-1.560.3355150.316736237710
1.56-1.580.3395230.290549451714
1.58-1.60.2943430.281574678922
1.6-1.620.368670.26881173124034
1.62-1.650.3177720.26151601167346
1.65-1.680.35931210.26142026214759
1.68-1.710.28741450.25072426257171
1.71-1.740.26371220.24942674279677
1.74-1.770.28431220.24412806292881
1.77-1.810.28371490.23042937308685
1.81-1.850.22541500.21693083323388
1.85-1.890.241780.21163250342894
1.89-1.940.26042060.20093383358999
1.94-1.990.20811770.191134763653100
1.99-2.050.22021860.186134603646100
2.05-2.110.19071930.178334563649100
2.11-2.190.19451830.177234863669100
2.19-2.280.17882050.170534583663100
2.28-2.380.20812150.162434733688100
2.38-2.50.21042210.160934393660100
2.5-2.660.17452320.164234553687100
2.66-2.870.19261820.168635123694100
2.87-3.160.191630.162335403703100
3.16-3.610.16931650.157335703735100
3.61-4.550.17681410.155536283769100
4.55-49.520.21272120.194337133925100
Refinement TLS params.Method: refined / Origin x: 30.1267 Å / Origin y: 4.0871 Å / Origin z: 19.0783 Å
111213212223313233
T0.1723 Å2-0.0165 Å2-0.0099 Å2-0.1508 Å2-0.0564 Å2--0.1544 Å2
L1.787 °2-0.3232 °2-0.1999 °2--0.0343 °2-0.0846 °2---0.0769 °2
S0.0174 Å °-0.0345 Å °0.0066 Å °0.0048 Å °-0.0104 Å °0.0072 Å °0.0142 Å °0.0023 Å °-0.0097 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA829 - 1011
2X-RAY DIFFRACTION1allB829 - 1011
3X-RAY DIFFRACTION1allC15 - 92
4X-RAY DIFFRACTION1allD15 - 92
5X-RAY DIFFRACTION1allS1 - 312

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