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- PDB-3zgk: NMR solution structure of the RXLR effector AVR3a11 from Phytopht... -

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Basic information

Entry
Database: PDB / ID: 3zgk
TitleNMR solution structure of the RXLR effector AVR3a11 from Phytophthora Capsici
ComponentsAVR3A11
KeywordsPROTEIN BINDING / PLANT DISEASES / RXLR
Function / homologyArc Repressor Mutant, subunit A - #2460 / RXLR phytopathogen effector protein / RXLR phytopathogen effector protein, Avirulence activity / Arc Repressor Mutant, subunit A / Orthogonal Bundle / extracellular region / Mainly Alpha / RxLR effector protein
Function and homology information
Biological speciesPHYTOPHTHORA CAPSICI (eukaryote)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsTolchard, J. / Chambers, V.S. / Boutemy, L.S. / Gathercole, R.L. / Banfield, M.J. / Blumenschein, T.M.
CitationJournal: To be Published
Title: NMR Solution Structure of the Avr3A11 from Phytophthora Capsi
Authors: Tolchard, J. / Chambers, V.S. / Boutemy, L.S. / Gathercole, R.L. / Banfield, M.J. / Blumenschein, T.M.
History
DepositionDec 18, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2014Provider: repository / Type: Initial release
Revision 2.0Apr 3, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Other / Structure summary
Category: atom_site / audit_author ...atom_site / audit_author / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc / pdbx_database_status / pdbx_nmr_representative / pdbx_validate_close_contact / pdbx_validate_planes / pdbx_validate_torsion
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.pdbx_auth_atom_name / _audit_author.name / _citation_author.name / _pdbx_database_status.recvd_author_approval / _pdbx_nmr_representative.conformer_id / _pdbx_validate_close_contact.PDB_model_num / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_close_contact.dist / _pdbx_validate_planes.PDB_model_num / _pdbx_validate_planes.rmsd / _pdbx_validate_torsion.PDB_model_num / _pdbx_validate_torsion.auth_comp_id / _pdbx_validate_torsion.auth_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi
Revision 2.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 2.2Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AVR3A11


Theoretical massNumber of molelcules
Total (without water)8,2671
Polymers8,2671
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein AVR3A11


Mass: 8267.472 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PHYTOPHTHORA CAPSICI (eukaryote) / Plasmid: POPIN-F / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G1K3S4
Sequence detailsTHE 3ZGK SEQUENCE IS MAPPED TO THE CLOSEST UNIPROT REFERENCE G1K3S4. AUTHOR SUGGESTS THAT RESIDUES ...THE 3ZGK SEQUENCE IS MAPPED TO THE CLOSEST UNIPROT REFERENCE G1K3S4. AUTHOR SUGGESTS THAT RESIDUES 63-69 IN THE COORDINATES ARE ACTUALLY FROM THE WILD TYPE PROTEIN.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111H-15N HSQC
1211H-13C HSQC
1311H-15N NOESY
1411H-13C NOESY
151CBCA(CO)NH
161HN(CA)CB
171CC(CO)NH
181H(CCO)NH
1911H-15N TOCSY
1101AROMATIC 1H-13C TROSY
1111(HB)CB(CGCDCE)HE
NMR detailsText: NONE

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Sample preparation

DetailsContents: 10% WATER/90% D2O, 200 MICROM DSS, 0.02% NAN3
Sample conditionsIonic strength: 150 mM / pH: 8.8 / Pressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.3BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
NMRPipestructure solution
CcpNmr AnalysisANALYSISstructure solution
UNIOstructure solution
CYANAstructure solution
CNS USING RECOORD SCRIPTSSCRIPTSstructure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
Details: STRUCTURES WERE CALCULATED USING THE SCRIPTS FROM THE RECOORD DATABASE
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 20

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