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- PDB-5a6p: Heavy metal associated domain of NLR-type immune receptor Pikp1 f... -

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Basic information

Entry
Database: PDB / ID: 5a6p
TitleHeavy metal associated domain of NLR-type immune receptor Pikp1 from rice (Oryza sativa)
ComponentsRESISTANCE PROTEIN PIKP-1
KeywordsIMMUNE SYSTEM / HEAVY METAL ASSOCIATED DOMAIN / NLR IMMUNE RECEPTOR
Function / homology
Function and homology information


defense response to other organism / ADP binding / ATP hydrolysis activity / metal ion binding
Similarity search - Function
Rx, N-terminal / Rx N-terminal domain / Disease resistance protein, plants / NB-ARC / NB-ARC domain / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily ...Rx, N-terminal / Rx N-terminal domain / Disease resistance protein, plants / NB-ARC / NB-ARC domain / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat domain superfamily / Alpha-Beta Plaits / Winged helix-like DNA-binding domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Resistance protein Pikp-1
Similarity search - Component
Biological speciesORYZA SATIVA (Asian cultivated rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsMaqbool, A. / Saitoh, H. / Franceschetti, M. / Stevenson, C.E. / Uemura, A. / Kanzaki, H. / Kamoun, S. / Terauchi, R. / Banfield, M.J.
CitationJournal: Elife / Year: 2015
Title: Structural basis of pathogen recognition by an integrated HMA domain in a plant NLR immune receptor.
Authors: Maqbool, A. / Saitoh, H. / Franceschetti, M. / Stevenson, C.E. / Uemura, A. / Kanzaki, H. / Kamoun, S. / Terauchi, R. / Banfield, M.J.
History
DepositionJun 30, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Mar 22, 2017Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RESISTANCE PROTEIN PIKP-1
B: RESISTANCE PROTEIN PIKP-1


Theoretical massNumber of molelcules
Total (without water)15,6322
Polymers15,6322
Non-polymers00
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-3.3 kcal/mol
Surface area7820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.650, 54.650, 235.220
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein RESISTANCE PROTEIN PIKP-1 / NLR IMMUNE RECEPTOR


Mass: 7816.232 Da / Num. of mol.: 2
Fragment: HEAVY METAL ASSOCIATED DOMAIN, UNP RESIDUES 186-258
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ORYZA SATIVA (Asian cultivated rice) / Strain: K60 / Plasmid: POPINS3C / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: E9KPB5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 62 % / Description: NONE
Crystal growDetails: PROTEIN WAS CRYSTALLLIZED WITH 0.1M MIB BUFFER, PH 5.0 AND 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.2
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Apr 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.1→47.33 Å / Num. obs: 12356 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 45 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 32.3
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 46.8 % / Rmerge(I) obs: 1.17 / Mean I/σ(I) obs: 4.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
AutoSolwizard inphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.1→47.33 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / SU B: 8.299 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES. ASPARAGINE 200 IS DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.22904 691 5.3 %RANDOM
Rwork0.20201 ---
obs0.20354 12356 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.756 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20.14 Å20 Å2
2--0.28 Å20 Å2
3----0.9 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1063 0 0 44 1107
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191064
X-RAY DIFFRACTIONr_bond_other_d0.0010.021152
X-RAY DIFFRACTIONr_angle_refined_deg1.7922.0211422
X-RAY DIFFRACTIONr_angle_other_deg0.81532653
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0345142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.08325.33330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.1415218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.846156
X-RAY DIFFRACTIONr_chiral_restr0.1010.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021147
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02183
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3042.738580
X-RAY DIFFRACTIONr_mcbond_other2.3062.738579
X-RAY DIFFRACTIONr_mcangle_it3.4014.064718
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8393.256484
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.19 44 -
Rwork0.206 861 -
obs--99.89 %
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)
12.64920.9237-0.72484.57250.31672.7164-0.08540.2262-0.3944-0.1075-0.10520.37190.1499-0.06970.19060.36060.1698-0.00590.1602-0.13580.239521.246924.3992100.7793
22.9264-0.2869-1.0633.27931.23425.06730.0261-0.1278-0.28590.4423-0.03130.29030.39770.16580.00520.34810.07290.02160.0617-0.03350.098618.143637.1636114.7029
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A186 - 258
2X-RAY DIFFRACTION2B184 - 258

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