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- PDB-5frk: SeMet crystal structure of Erwinia amylovora AmyR amylovoran repr... -

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Basic information

Entry
Database: PDB / ID: 5frk
TitleSeMet crystal structure of Erwinia amylovora AmyR amylovoran repressor, a member of the YbjN protein family
ComponentsAMYR
KeywordsTRANSCRIPTION / AMYLOVORAN / YBJN / FIRE BLIGHT / PLANT PATHOGEN / T3SS
Function / homologyPutative sensory transduction regulator YbjN / Putative bacterial sensory transduction regulator / Uncharacterized protein ybjN
Function and homology information
Biological speciesERWINIA AMYLOVORA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.12 Å
AuthorsBartho, J.D. / Bellini, D. / Wuerges, J. / Demitri, N. / Walsh, M. / Benini, S.
CitationJournal: PLoS ONE / Year: 2017
Title: The crystal structure of Erwinia amylovora AmyR, a member of the YbjN protein family, shows similarity to type III secretion chaperones but suggests different cellular functions.
Authors: Bartho, J.D. / Bellini, D. / Wuerges, J. / Demitri, N. / Toccafondi, M. / Schmitt, A.O. / Zhao, Y. / Walsh, M.A. / Benini, S.
History
DepositionDec 18, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2Mar 6, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / pdbx_seq_map_depositor_info / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AMYR
B: AMYR


Theoretical massNumber of molelcules
Total (without water)36,9302
Polymers36,9302
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-19.8 kcal/mol
Surface area13520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.028, 49.618, 57.813
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein AMYR / PROTEIN YBJN


Mass: 18464.859 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ERWINIA AMYLOVORA (bacteria) / Strain: CFBP1430 / Plasmid: PETM-11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D4I047
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsN-TERMINAL GA ADDED FROM TEV PROTEASE CLEAVAGE SITE. H2G MUTATION A CLONING ARTEFACT.

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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: 3.29 Å3/Da / Density % sol: 62.66 % / Description: NONE
Crystal growTemperature: 293 K / pH: 7.3
Details: 0.1 M SODIUM CACODYLATE PH7.3 0.3 M MAGNESIUM CHLORIDE, 42% PEG 200, 293 K PROTEIN CONCENTRATION 8 MG/ML

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9796
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.12→53.34 Å / Num. obs: 22681 / % possible obs: 97.2 % / Observed criterion σ(I): 2 / Redundancy: 12.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 24
Reflection shellResolution: 2.12→2.18 Å / Redundancy: 8.9 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.4 / % possible all: 75.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.12→69.01 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.915 / SU B: 6.146 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. INSUFFICIENT EVIDENCE TO CONFIRM TETRAMERIC STATE IN SOLUTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.27584 1142 5.1 %RANDOM
Rwork0.21593 ---
obs0.21887 21056 95.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.904 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20 Å2
2--2.58 Å20 Å2
3----2.26 Å2
Refinement stepCycle: LAST / Resolution: 2.12→69.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2218 0 0 75 2293
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192262
X-RAY DIFFRACTIONr_bond_other_d0.0010.022192
X-RAY DIFFRACTIONr_angle_refined_deg1.7781.9853072
X-RAY DIFFRACTIONr_angle_other_deg0.8213.0025041
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1485287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.50626.12993
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.07115346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.85153
X-RAY DIFFRACTIONr_chiral_restr0.0970.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022540
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02483
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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: 2.119→2.174 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.553 73 -
Rwork0.523 1058 -
obs--66.49 %

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