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- PDB-6hqz: Crystal structure of the type III effector protein AvrRpt2 from E... -

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Basic information

Entry
Database: PDB / ID: 6hqz
TitleCrystal structure of the type III effector protein AvrRpt2 from Erwinia amylovora, a C70 family cysteine protease
ComponentsAvrRpt2
KeywordsHYDROLASE / Avirulence / resistance / plant pathogen / cysteine protease / effector / T3ss
Function / homologyPeptidase C70, AvrRpt2 / Papain-like cysteine protease AvrRpt2 / AvrRpt2
Function and homology information
Biological speciesErwinia amylovora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsBartho, J.D. / Demitri, N. / Wuerges, J. / Benini, S.
CitationJournal: J.Struct.Biol. / Year: 2019
Title: The structure of Erwinia amylovora AvrRpt2 provides insight into protein maturation and induced resistance to fire blight by Malus × robusta 5.
Authors: Bartho, J.D. / Demitri, N. / Bellini, D. / Flachowsky, H. / Peil, A. / Walsh, M.A. / Benini, S.
History
DepositionSep 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 23, 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

Downloads & links

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Assembly

Deposited unit
A: AvrRpt2
B: AvrRpt2


Theoretical massNumber of molelcules
Total (without water)34,9902
Polymers34,9902
Non-polymers00
Water1,63991
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-2 kcal/mol
Surface area15330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.313, 63.884, 85.983
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 AvrRpt2


Mass: 17494.756 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: In this construct the protein sequence starts from G70, N69 is a result of the cloning procedure and of subsequent tag cleavage. we report the structure of AvrRpt2_70-222. A S-S bridge is ...Details: In this construct the protein sequence starts from G70, N69 is a result of the cloning procedure and of subsequent tag cleavage. we report the structure of AvrRpt2_70-222. A S-S bridge is formed between C156 of chain A and C156 of chain B
Source: (gene. exp.) Erwinia amylovora (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2U7NR52
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 9
Details: 100 mM TRIS-HCL pH 9.0 10% glycerol, 100 mM sodium cacodylate, 15% PEG 6K
Temp details: vibration free incubator

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.064 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.064 Å / Relative weight: 1
ReflectionResolution: 1.8→51.32 Å / Num. obs: 28980 / % possible obs: 99.02 % / Redundancy: 2.8 % / Rrim(I) all: 0.054 / Net I/σ(I): 13.4
Reflection shellResolution: 1.8→1.85 Å / Num. unique obs: 2004 / Rrim(I) all: 0.664 / % possible all: 94.76

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XDSdata scaling
SHELXCDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→51.32 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.951 / SU B: 7.938 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.127 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23315 1536 5 %RANDOM
Rwork0.20944 ---
obs0.2106 28980 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.225 Å2
Baniso -1Baniso -2Baniso -3
1--2.94 Å2-0 Å20 Å2
2--2.52 Å2-0 Å2
3---0.42 Å2
Refinement stepCycle: 1 / Resolution: 1.8→51.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2454 0 0 91 2545
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192529
X-RAY DIFFRACTIONr_bond_other_d0.0020.022223
X-RAY DIFFRACTIONr_angle_refined_deg1.8651.953436
X-RAY DIFFRACTIONr_angle_other_deg1.13335173
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0235308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.66123.435131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.91715407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5551524
X-RAY DIFFRACTIONr_chiral_restr0.120.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212863
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02533
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_it1.2582.2081232
X-RAY DIFFRACTIONr_mcbond_other1.2572.2071231
X-RAY DIFFRACTIONr_mcangle_it1.8883.3041537
X-RAY DIFFRACTIONr_mcangle_other1.8883.3051538
X-RAY DIFFRACTIONr_scbond_it1.5242.4051297
X-RAY DIFFRACTIONr_scbond_other1.5252.4041294
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3933.531897
X-RAY DIFFRACTIONr_long_range_B_refined4.14325.9322763
X-RAY DIFFRACTIONr_long_range_B_other4.11825.7982753
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.803→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 110 -
Rwork0.355 2004 -
obs--94.76 %
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)
13.6491-0.28681.05042.930.06343.7842-0.03170.0919-0.3492-0.2549-0.0196-0.04370.2307-0.00260.05130.0651-0.0266-0.00240.02870.01450.064638.43629.64774.5187
24.0096-0.99671.45922.5934-0.67772.1109-0.10030.30950.3562-0.0240.05860.1098-0.24070.01280.04170.1218-0.0542-0.03410.09860.09650.1069.504-2.399221.321
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A69 - 222
2X-RAY DIFFRACTION2B69 - 222

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