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- PDB-5zc3: The Crystal Structure of PcRxLR12 -

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Basic information

Entry
Database: PDB / ID: 5zc3
TitleThe Crystal Structure of PcRxLR12
ComponentsRxLR effector
KeywordsIMMUNOSUPPRESSANT / RxLR effectors
Function / homologyEffector PexRD54, WY-domain / RxLR effector
Function and homology information
Biological speciesPhytophthora capsici (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.005 Å
AuthorsZhao, L. / Zhang, X. / Zhu, C.
Funding support China, 1items
OrganizationGrant numberCountry
the National Natural Science Foundation of Chinathe National Natural Science Foundation of China China
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Crystal structure of the RxLR effector PcRxLR12 from Phytophthora capsici
Authors: Zhao, L. / Zhang, X. / Zhang, X. / Song, W. / Li, X. / Feng, R. / Yang, C. / Huang, Z. / Zhu, C.
History
DepositionFeb 14, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: RxLR effector
A: RxLR effector


Theoretical massNumber of molelcules
Total (without water)107,1102
Polymers107,1102
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-1 kcal/mol
Surface area43460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.532, 78.308, 179.057
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 RxLR effector


Mass: 53555.082 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phytophthora capsici (eukaryote) / Strain: SD33 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A3F2YLV0*PLUS
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: 2.14 Å3/Da / Density % sol: 42.68 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100mM HEPES pH 7.5, 6%(w/v) PEG 6000 and 5%(v/v) -2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 3→47 Å / Num. obs: 19409 / % possible obs: 99.8 % / Redundancy: 7.1 % / Net I/σ(I): 32.3
Reflection shellResolution: 3→3.1 Å / Redundancy: 6.9 % / Num. unique obs: 1622 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: SAD / Resolution: 3.005→47 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.74
RfactorNum. reflection% reflection
Rfree0.2603 987 5.09 %
Rwork0.2095 --
obs0.2121 19409 97.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 48.48 Å2
Refinement stepCycle: LAST / Resolution: 3.005→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6622 0 0 0 6622
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066750
X-RAY DIFFRACTIONf_angle_d1.0669113
X-RAY DIFFRACTIONf_dihedral_angle_d15.9582479
X-RAY DIFFRACTIONf_chiral_restr0.0421046
X-RAY DIFFRACTIONf_plane_restr0.0061131
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.005-3.16320.3639154248895
3.1632-3.36130.34821300.2545256096
3.3613-3.62070.26141380.2311257997
3.6207-3.98490.34241420.2064260998
3.9849-4.56120.23591390.1796263998
4.5612-5.7450.20311490.19482701100
5.7450.20121350.1898284699
Refinement TLS params.Method: refined / Origin x: 137.2092 Å / Origin y: 79.698 Å / Origin z: 196.3175 Å
111213212223313233
T0.2815 Å20.0007 Å2-0.0026 Å2-0.2073 Å20.0097 Å2--0.2773 Å2
L0.2671 °20.0296 °2-0.1111 °2-0.0037 °2-0.0373 °2--0.3596 °2
S-0.0053 Å °-0.0534 Å °-0.0433 Å °0.0255 Å °0.0115 Å °-0.0096 Å °0.0996 Å °0.0183 Å °-0.0092 Å °
Refinement TLS groupSelection details: all

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