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- PDB-3tjy: Structure of the Pto-binding domain of HopPmaL generated by limit... -

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Basic information

Entry
Database: PDB / ID: 3tjy
TitleStructure of the Pto-binding domain of HopPmaL generated by limited chymotrypsin digestion
ComponentsEffector protein hopAB3
KeywordsSIGNALING PROTEIN / type III effector / HopPmaL / Pseudomonas syringae / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / helical bundle / Pto
Function / homology
Function and homology information


symbiont-mediated perturbation of host programmed cell death / extracellular region
Similarity search - Function
Monooxygenase - #110 / Effector protein HopAB, BAK1-binding domain / Effector protein HopAB, BAK1-binding domain superfamily / Avirulence AvrPtoB, BAK1-binding domain / Effector protein HopAB, Pto-binding domain / Monooxygenase / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Effector protein hopAB3
Similarity search - Component
Biological speciesPseudomonas syringae pv. maculicola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsSinger, A.U. / Stein, A. / Xu, X. / Cui, H. / Joachimiak, A. / Edwards, A.M. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Biochemistry / Year: 2012
Title: Structural analysis of HopPmaL reveals the presence of a second adaptor domain common to the HopAB family of Pseudomonas syringae type III effectors.
Authors: Singer, A.U. / Wu, B. / Yee, A. / Houliston, S. / Xu, X. / Cui, H. / Skarina, T. / Garcia, M. / Semesi, A. / Arrowsmith, C.H. / Savchenko, A.
History
DepositionAug 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Jan 9, 2013Group: Database references
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Effector protein hopAB3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0868
Polymers10,6561
Non-polymers4307
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.427, 57.427, 54.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Effector protein hopAB3 / Avirulence protein hopPmaL


Mass: 10655.572 Da / Num. of mol.: 1 / Fragment: HopPmaL / Mutation: none
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. maculicola (bacteria)
Strain: ES4326 / Gene: hopAB3, hopPmaL / Plasmid: p15TvLic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)-RIPL / References: UniProt: Q8RP04
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsPROTEIN WAS CLONED AS HOPPMAL RESIDUES 135-273, CUT WITH TEV, THEN TREATED WITH LIMITING AMOUNTS OF ...PROTEIN WAS CLONED AS HOPPMAL RESIDUES 135-273, CUT WITH TEV, THEN TREATED WITH LIMITING AMOUNTS OF THERMOLYSIN DURING CRYSTALLIZATION

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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: 2.12 Å3/Da / Density % sol: 41.98 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris pH 6.5 plus 1.5M Ammonium Sulphate. 0.03 mg/ml chymotrypsin was added to the protein prior to adding crystallization liquor. Crystals were cryoprotected with Paratone-N oil , ...Details: 0.1M Bis-Tris pH 6.5 plus 1.5M Ammonium Sulphate. 0.03 mg/ml chymotrypsin was added to the protein prior to adding crystallization liquor. Crystals were cryoprotected with Paratone-N oil , VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97942 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2009 / Details: mirrors
RadiationMonochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.65→25.682 Å / Num. all: 11562 / Num. obs: 11555 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.3 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 42.133
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 3.7 / Rsym value: 0.501 / % possible all: 100

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7.1_743) / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 1.7→25.682 Å / SU ML: 0.42 / σ(F): 1.35 / Phase error: 17.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2174 510 4.83 %
Rwork0.188 --
obs0.1894 10558 99.97 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.325 Å2 / ksol: 0.39 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.1431 Å20 Å2-0 Å2
2--0.1431 Å20 Å2
3----0.2863 Å2
Refinement stepCycle: LAST / Resolution: 1.7→25.682 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms612 0 19 80 711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009708
X-RAY DIFFRACTIONf_angle_d1.152961
X-RAY DIFFRACTIONf_dihedral_angle_d13.952282
X-RAY DIFFRACTIONf_chiral_restr0.079103
X-RAY DIFFRACTIONf_plane_restr0.005132
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7002-1.87130.27091300.22512439X-RAY DIFFRACTION100
1.8713-2.1420.16971280.17032465X-RAY DIFFRACTION100
2.142-2.69820.22041340.16132486X-RAY DIFFRACTION100
2.6982-25.68510.22091180.19932658X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -14.4761 Å / Origin y: -4.9353 Å / Origin z: 13.9018 Å
111213212223313233
T0.0621 Å2-0.0013 Å2-0.0138 Å2-0.0126 Å20.0166 Å2--0.08 Å2
L2.3437 °20.6889 °2-0.1946 °2-2.0583 °20.8467 °2--3.0152 °2
S0.0033 Å °-0.0683 Å °-0.4344 Å °0.1066 Å °-0.0207 Å °-0.2411 Å °0.3413 Å °-0.0472 Å °0.026 Å °
Refinement TLS groupSelection details: (chain A and resid 140:217)

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