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- PDB-8i3x: Rice APIP6-RING homodimer -

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Basic information

Entry
Database: PDB / ID: 8i3x
TitleRice APIP6-RING homodimer
ComponentsRING-type domain-containing protein
KeywordsTRANSFERASE / rice / E3 ubiquitin transferases/ligase
Function / homologyE3 ubiquitin-protein ligase RFI2 / Ring finger domain / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / ubiquitin-protein transferase activity / Zinc finger, RING/FYVE/PHD-type / metal ion binding / RING-type domain-containing protein
Function and homology information
Biological speciesOryza sativa (Asian cultivated rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsZheng, Y. / Zhang, X. / Liu, Y. / Liu, J. / Wang, D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32030089 China
CitationJournal: Phytopathol Res / Year: 2023
Title: Crystal structure of rice APIP6 reveals a new dimerization mode of RING-type E3 ligases that facilities the construction of its working model
Authors: Zheng, Y. / Zhang, X. / Liu, Y. / Zhu, T. / Wu, X. / Ning, Y. / Liu, J. / Wang, D.
History
DepositionJan 18, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RING-type domain-containing protein
B: RING-type domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9276
Polymers15,6662
Non-polymers2624
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-7 kcal/mol
Surface area6570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.239, 46.577, 83.182
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RING-type domain-containing protein


Mass: 7832.927 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Gene: OsI_18510 / Production host: Escherichia coli (E. coli) / References: UniProt: B8AY66
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.12 Å3/Da / Density % sol: 41.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: ammonium fluoride, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.78→40.64 Å / Num. obs: 13316 / % possible obs: 99.89 % / Redundancy: 12.1 % / CC1/2: 0.994 / Net I/σ(I): 40.5
Reflection shellResolution: 1.78→1.844 Å / Num. unique obs: 1294 / CC1/2: 0.988

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→40.64 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2318 620 4.66 %
Rwork0.1856 --
obs0.1878 13305 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.78→40.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms892 0 4 90 986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005902
X-RAY DIFFRACTIONf_angle_d0.7431212
X-RAY DIFFRACTIONf_dihedral_angle_d3.327536
X-RAY DIFFRACTIONf_chiral_restr0.057132
X-RAY DIFFRACTIONf_plane_restr0.004158
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7801-1.95920.23381500.23383095X-RAY DIFFRACTION100
1.9592-2.24270.24431500.19563127X-RAY DIFFRACTION100
2.2427-2.82540.23551590.22373149X-RAY DIFFRACTION100
2.8254-40.640.22811610.16713314X-RAY DIFFRACTION100
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)
17.14043.9909-0.41723.33961.13042.5997-0.11090.0255-0.62560.2649-0.0973-0.4022-0.308-0.51060.35960.3330.03830.00990.320.00310.47036.2503-10.2464-18.9976
22.1907-1.10640.65443.2261-3.0763.11880.1506-0.464-0.28031.14920.0448-0.4999-0.14410.8356-0.18020.51140.0277-0.04340.3828-0.01180.533210.012-7.6808-16.1683
36.77091.60040.38812.32360.45439.75640.2202-0.6009-1.42960.2913-0.0438-0.85731.33890.76990.05070.52340.080.0030.31630.03660.69878.3048-4.6529-10.649
44.8114.14940.00733.7192-0.38461.0521-0.25260.2197-0.0429-0.25840.3920.98250.5594-0.9321-0.26530.3576-0.0687-0.01660.37930.020.4489-4.6867-5.4973-15.0321
53.68130.42130.71813.90070.23761.9017-0.1019-0.02550.0919-0.20820.07490.003-0.10250.05310.02880.3221-0.00820.00750.2594-0.03430.31491.7912.4146-18.1996
68.4649-0.8310.13217.32271.07247.4846-0.04090.1661-0.5378-0.3774-0.20590.83550.2528-0.04680.19060.41860.0110.01450.2568-0.02720.4695-5.4094-4.0266-22.8165
76.84324.20341.90032.89432.3745.37570.1516-0.07060.19420.7251-0.1920.94150.2946-0.1220.14810.40760.0770.02390.326-0.030.446-4.79928.8074-13.9129
88.7688-1.45176.51193.42-3.41328.60770.4185-0.9772-0.62210.7781-0.07130.40490.4471-0.4659-0.68570.8453-0.00990.04350.5860.01960.3761-0.67780.84312.7217
92.0852-1.1094-2.44217.1577-0.11089.6951-0.33890.5841-0.5712-0.3583-0.06051.3090.7653-0.6690.14490.6923-0.11630.09460.5599-0.09690.5118-4.43640.7279-1.2051
100.70021.72750.02217.65251.79778.06290.1367-1.1631-2.02960.12440.27120.90551.1463-0.9269-0.29390.5303-0.0607-0.02260.46740.09130.5958-2.5667-2.0171-7.073
111.34562.1501-1.64673.5235-2.00498.1853-1.0997-0.61430.81820.55180.1482-1.37150.45980.80780.69510.44580.1264-0.20360.64390.08570.5210.4661-0.4858-2.6666
129.05891.0827-0.59993.1027-0.23654.17210.0858-0.68330.43070.15290.0607-0.0097-0.11180.2196-0.1190.37450.0220.00050.2904-0.0610.3074.9947.5364-7.151
133.1326-0.4195-1.07114.0269-0.51485.5857-1.1338-1.79010.48742.36671.04870.6378-0.20230.62280.06450.86330.18210.06640.6388-0.02640.406611.6467.00830.8901
142.9428-4.27043.90549.5433-2.46519.71030.1574-0.06970.6942-0.03470.0363-0.7023-0.1570.6203-0.10380.3084-0.0493-0.00170.3813-0.03040.372111.93727.396-14.4532
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 36 )
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 46 )
3X-RAY DIFFRACTION3chain 'A' and (resid 47 through 53 )
4X-RAY DIFFRACTION4chain 'A' and (resid 54 through 58 )
5X-RAY DIFFRACTION5chain 'A' and (resid 59 through 77 )
6X-RAY DIFFRACTION6chain 'A' and (resid 78 through 82 )
7X-RAY DIFFRACTION7chain 'A' and (resid 83 through 91 )
8X-RAY DIFFRACTION8chain 'B' and (resid 32 through 36 )
9X-RAY DIFFRACTION9chain 'B' and (resid 37 through 46 )
10X-RAY DIFFRACTION10chain 'B' and (resid 47 through 53 )
11X-RAY DIFFRACTION11chain 'B' and (resid 54 through 58 )
12X-RAY DIFFRACTION12chain 'B' and (resid 59 through 77 )
13X-RAY DIFFRACTION13chain 'B' and (resid 78 through 82 )
14X-RAY DIFFRACTION14chain 'B' and (resid 83 through 91 )

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