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- PDB-8rqi: Structure of Rhizobium NopD with ubiquitin -

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Basic information

Entry
Database: PDB / ID: 8rqi
TitleStructure of Rhizobium NopD with ubiquitin
Components
  • NopD
  • Polyubiquitin-B
KeywordsHYDROLASE / Protease / deubiquitinase / rhizobium / ubiquitin
Function / homology
Function and homology information


deNEDDylase activity / protein deneddylation / symbiont entry into host cell via disruption of host cell glycocalyx / symbiont entry into host cell via disruption of host cell envelope / virus tail / cysteine-type peptidase activity / proteolysis
Similarity search - Function
NEDD8-specific protease 1/2-like / Ulp1 protease family, C-terminal catalytic domain / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Pectin lyase fold / Pectin lyase fold/virulence factor / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
prop-2-en-1-amine / Type III effector / Tail fiber
Similarity search - Component
Biological speciesBradyrhizobium (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsReverter, D. / Li, Y.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and Universities Spain
CitationJournal: Commun Biol / Year: 2024
Title: Broad-spectrum ubiquitin/ubiquitin-like deconjugation activity of the rhizobial effector NopD from Bradyrhizobium (sp. XS1150).
Authors: Li, Y. / Perez-Gil, J. / Lois, L.M. / Varejao, N. / Reverter, D.
History
DepositionJan 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 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: NopD
B: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9473
Polymers35,8902
Non-polymers571
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-10 kcal/mol
Surface area11700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.496, 86.496, 46.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein NopD


Mass: 27370.529 Da / Num. of mol.: 1
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 Polyubiquitin-B


Mass: 8519.778 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#3: Chemical ChemComp-AYE / prop-2-en-1-amine / ALLYLAMINE


Mass: 57.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7N / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.43 Å3/Da / Density % sol: 49.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M imidazole 8.0 and 10% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.94→43.25 Å / Num. obs: 25728 / % possible obs: 94.2 % / Redundancy: 6.8 % / CC1/2: 0.997 / Net I/σ(I): 13.3
Reflection shellResolution: 1.942→2.043 Å / Num. unique obs: 1141 / CC1/2: 0.51

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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-2

Resolution: 1.94→43.25 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1994 1173 5.15 %
Rwork0.1716 21597 -
obs0.173 22770 88.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.72 Å2 / Biso mean: 59.7409 Å2 / Biso min: 30.56 Å2
Refinement stepCycle: final / Resolution: 1.94→43.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 4 58 2121
Biso mean--47.21 54.51 -
Num. residues----258
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.94-2.030.3449340.309685088428
2.03-2.140.30241670.25592384255180
2.14-2.270.28041630.23272987315099
2.27-2.450.26711520.209830663218100
2.45-2.690.26941550.20530483203100
2.69-3.080.22411620.206530553217100
3.08-3.880.20951720.176130633235100
3.88-43.250.14581680.13331443312100
Refinement TLS params.Method: refined / Origin x: -13.7594 Å / Origin y: 35.3854 Å / Origin z: -2.8502 Å
111213212223313233
T0.3216 Å2-0.0005 Å20.0335 Å2-0.3493 Å20.0484 Å2--0.2906 Å2
L4.6878 °2-0.7446 °20.7477 °2-3.3995 °2-0.4458 °2--1.9654 °2
S-0.1878 Å °-0.128 Å °-0.4111 Å °0.1053 Å °0.1246 Å °0.3504 Å °0.0272 Å °0.2008 Å °0.0529 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA828 - 1011
2X-RAY DIFFRACTION1allB1 - 76
3X-RAY DIFFRACTION1allS1 - 59

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