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- PDB-4m70: Crystal structure of potato Rx-CC domain in complex with RanGAP2-... -

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Basic information

Entry
Database: PDB / ID: 4m70
TitleCrystal structure of potato Rx-CC domain in complex with RanGAP2-WPP domain
Components
  • (Ran GTPase activating protein 2) x 2
  • Rx protein
KeywordsPLANT PROTEIN / Rx / RanGAP2 / coiled coil domain / WPP domain / plant disease resistance gene / resistance responses / popato X virus
Function / homology
Function and homology information


ADP binding / defense response
Similarity search - Function
WPP domain / WPP domain / WPP domain superfamily / WPP domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4130 / Virus X resistance protein-like, coiled-coil domain / NB-ARC / NB-ARC domain / Leucine Rich repeat / Serum Albumin; Chain A, Domain 1 ...WPP domain / WPP domain / WPP domain superfamily / WPP domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4130 / Virus X resistance protein-like, coiled-coil domain / NB-ARC / NB-ARC domain / Leucine Rich repeat / Serum Albumin; Chain A, Domain 1 / Leucine-rich repeat / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Leucine-rich repeat domain superfamily / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ran GTPase activating protein 2 / Rx protein
Similarity search - Component
Biological speciesSolanum tuberosum (potato)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.103 Å
AuthorsChai, J. / Hao, W.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural Basis for the Interaction between the Potato Virus X Resistance Protein (Rx) and Its Cofactor Ran GTPase-activating Protein 2 (RanGAP2)
Authors: Hao, W. / Collier, S.M. / Moffett, P. / Chai, J.
History
DepositionAug 12, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references
Revision 1.2Jun 28, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rx protein
E: Ran GTPase activating protein 2
L: Rx protein
J: Ran GTPase activating protein 2
I: Rx protein
B: Ran GTPase activating protein 2
H: Rx protein
Q: Rx protein
K: Ran GTPase activating protein 2
R: Ran GTPase activating protein 2


Theoretical massNumber of molelcules
Total (without water)125,93910
Polymers125,93910
Non-polymers00
Water3,135174
1
A: Rx protein
R: Ran GTPase activating protein 2


Theoretical massNumber of molelcules
Total (without water)23,6942
Polymers23,6942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-15 kcal/mol
Surface area9300 Å2
MethodPISA
2
E: Ran GTPase activating protein 2
L: Rx protein


Theoretical massNumber of molelcules
Total (without water)25,5612
Polymers25,5612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-17 kcal/mol
Surface area10840 Å2
MethodPISA
3
J: Ran GTPase activating protein 2
I: Rx protein


Theoretical massNumber of molelcules
Total (without water)25,5612
Polymers25,5612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-18 kcal/mol
Surface area10450 Å2
MethodPISA
4
B: Ran GTPase activating protein 2
H: Rx protein


Theoretical massNumber of molelcules
Total (without water)25,5612
Polymers25,5612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-16 kcal/mol
Surface area10720 Å2
MethodPISA
5
Q: Rx protein
K: Ran GTPase activating protein 2


Theoretical massNumber of molelcules
Total (without water)25,5612
Polymers25,5612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-11 kcal/mol
Surface area9480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.085, 91.142, 87.762
Angle α, β, γ (deg.)90.00, 101.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Rx protein


Mass: 14272.324 Da / Num. of mol.: 5 / Fragment: Rx-CC domain, UNP residues 1-122
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum tuberosum (potato) / Gene: rx / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9XGF5
#2: Protein
Ran GTPase activating protein 2


Mass: 11288.781 Da / Num. of mol.: 4 / Fragment: StRanGAP2-WPP domain, UNP residues 15-112
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum tuberosum (potato) / Gene: RanGAP2 / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / References: UniProt: I7JSB1
#3: Protein Ran GTPase activating protein 2


Mass: 9422.042 Da / Num. of mol.: 1 / Fragment: StRanGAP2-WPP domain, UNP residues 15-112
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others), (gene. exp.) Solanum tuberosum (potato)
Gene: RanGAP2, Rx / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / References: UniProt: I7JSB1
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF CHAIN R IS THE SAME OF CHAIN E, J, B, K. THE AUTHOR COULD OBSERVE RESIDUES 23-33, ...THE SEQUENCE OF CHAIN R IS THE SAME OF CHAIN E, J, B, K. THE AUTHOR COULD OBSERVE RESIDUES 23-33, 86-101 AND BELIEVED THAT THESE RESIDUES IS PART OF THE N- TERMINAL RESIDUES 15-37, C-TERMINAL RESIDUES 74-113. BUT THE AUTHOR IS NOT SURE WHICH PART CORRESPONDS WITH THESE RESIDUES. SO THE RESIDUE NUMBERS OF 23-33, 86-101 IS MEANINGLESS.

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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: 2.31 Å3/Da / Density % sol: 46.69 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10mM Tis, 100 mM NaCl, 39%(V/V) Tacsimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 10, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.103→28.648 Å / Num. all: 65379 / Num. obs: 65379 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 42.8 Å2 / Rmerge(I) obs: 0.053
Reflection shellResolution: 2.1→2.18 Å / % possible all: 97.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.103→28.648 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7001 / SU ML: 0.24 / σ(F): 0 / Phase error: 35.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2756 3325 5.09 %RANDOM
Rwork0.2529 62053 --
obs0.2541 65378 98.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.29 Å2 / Biso mean: 61.7444 Å2 / Biso min: 35.88 Å2
Refinement stepCycle: LAST / Resolution: 2.103→28.648 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7290 0 0 174 7464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067380
X-RAY DIFFRACTIONf_angle_d0.9439944
X-RAY DIFFRACTIONf_chiral_restr0.0551163
X-RAY DIFFRACTIONf_plane_restr0.0051260
X-RAY DIFFRACTIONf_dihedral_angle_d13.3442750
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1028-2.13280.41941160.34122398251491
2.1328-2.16460.37961310.32752474260595
2.1646-2.19840.34271250.30722518264396
2.1984-2.23450.29371310.31792543267496
2.2345-2.2730.3591290.34372516264596
2.273-2.31430.35151250.29542588271397
2.3143-2.35880.35321110.28092565267698
2.3588-2.40690.2911560.27152582273899
2.4069-2.45920.3171330.27522645277899
2.4592-2.51640.34071430.27562558270199
2.5164-2.57930.29911490.263526002749100
2.5793-2.6490.29831280.271726522780100
2.649-2.72690.31241600.270925822742100
2.7269-2.81480.29951520.270526092761100
2.8148-2.91530.261480.265926002748100
2.9153-3.03190.32331390.267326422781100
3.0319-3.16970.27811550.274626082763100
3.1697-3.33660.26731320.258226592791100
3.3366-3.54530.26831570.241325992756100
3.5453-3.81850.28251340.238526572791100
3.8185-4.20170.2081580.219926012759100
4.2017-4.80720.23621400.217726502790100
4.8072-6.04720.28181430.267126682811100
6.0472-28.65110.27391300.23382539266993

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