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- PDB-6inr: The crystal structure of phytoplasmal effector causing phyllody s... -

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Basic information

Entry
Database: PDB / ID: 6inr
TitleThe crystal structure of phytoplasmal effector causing phyllody symptoms 1 (PHYL1)
ComponentsPutative effector, AYWB SAP54-like protein
KeywordsGENE REGULATION / Phytoplasma / Phytoplasmal effector causing phyllody 1
Function / homologySequence-variable mosaic (SVM), signal sequence / SVM protein signal sequence / : / Putative effector, AYWB SAP54-like protein
Function and homology information
Biological species'Echinacea purpurea' witches'-broom phytoplasma (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.34 Å
AuthorsLiao, Y.T. / Lin, S.S. / Ko, T.P. / Wang, H.C.
Funding support Taiwan, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (Taiwan)107-2313-B-038-001 Taiwan
Ministry of Science and Technology (Taiwan)MOST106-2311-B-038-002 Taiwan
Ministry of Science and Technology (Taiwan)NSC103-2311-B-038-005-MY3 Taiwan
CitationJournal: Plant J. / Year: 2019
Title: Structural insights into the interaction between phytoplasmal effector causing phyllody 1 and MADS transcription factors.
Authors: Liao, Y.T. / Lin, S.S. / Lin, S.J. / Sun, W.T. / Shen, B.N. / Cheng, H.P. / Lin, C.P. / Ko, T.P. / Chen, Y.F. / Wang, H.C.
History
DepositionOct 26, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative effector, AYWB SAP54-like protein
B: Putative effector, AYWB SAP54-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0505
Polymers21,7122
Non-polymers3373
Water3,081171
1
A: Putative effector, AYWB SAP54-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0813
Polymers10,8561
Non-polymers2252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative effector, AYWB SAP54-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9692
Polymers10,8561
Non-polymers1121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.006, 65.006, 193.432
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-282-

HOH

21A-285-

HOH

31B-646-

HOH

41B-677-

HOH

51B-679-

HOH

61B-682-

HOH

71B-686-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 17 - 82 / Label seq-ID: 20 - 85

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Putative effector, AYWB SAP54-like protein


Mass: 10856.162 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) 'Echinacea purpurea' witches'-broom phytoplasma (bacteria)
Gene: EPWB_v1c1980 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0P7KHL3
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O

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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: 2.79 Å3/Da / Density % sol: 55.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.05 M cadmium sulfate hydrate, 0.1 M HEPES pH 7.5 and 1.0 M sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jul 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.34→20 Å / Num. obs: 10840 / % possible obs: 98.9 % / Redundancy: 8 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 44.6
Reflection shellResolution: 2.34→2.42 Å / Redundancy: 7.8 % / Rmerge(I) obs: 1.012 / Mean I/σ(I) obs: 2 / Num. unique obs: 1034 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data scaling
Blu-Icedata collection
BUCCANEERmodel building
HKL-2000data reduction
SHELXCDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.34→20 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.902 / Cross valid method: THROUGHOUT / ESU R: 0.424 / ESU R Free: 0.272 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27042 456 5 %RANDOM
Rwork0.25631 ---
obs0.25704 8698 83.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 47.451 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20.2 Å20 Å2
2--0.41 Å20 Å2
3----1.32 Å2
Refinement stepCycle: 1 / Resolution: 2.34→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1188 0 3 182 1373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021195
X-RAY DIFFRACTIONr_bond_other_d00.021216
X-RAY DIFFRACTIONr_angle_refined_deg1.2521.9861603
X-RAY DIFFRACTIONr_angle_other_deg3.47532809
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2065142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.28128.41363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.85615265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.932151
X-RAY DIFFRACTIONr_chiral_restr0.070.2188
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021344
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02243
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_it2.8854.536574
X-RAY DIFFRACTIONr_mcbond_other2.8774.533573
X-RAY DIFFRACTIONr_mcangle_it4.8666.781714
X-RAY DIFFRACTIONr_mcangle_other4.8636.783715
X-RAY DIFFRACTIONr_scbond_it3.3294.871619
X-RAY DIFFRACTIONr_scbond_other3.3264.871620
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8957.104890
X-RAY DIFFRACTIONr_long_range_B_refined10.04234.6411448
X-RAY DIFFRACTIONr_long_range_B_other9.97534.4711435
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 3698 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.24 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.34→2.401 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.485 17 -
Rwork0.351 262 -
obs--35.45 %

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