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- PDB-4g6t: Structure of the HopA1-SchA Chaperone-Effector Complex -

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Basic information

Entry
Database: PDB / ID: 4g6t
TitleStructure of the HopA1-SchA Chaperone-Effector Complex
Components
  • Type III chaperone protein ShcA
  • Type III effector HopA1
KeywordsCHAPERONE / Chaperone Effector / secretion chaperone
Function / homology
Function and homology information


protein secretion by the type III secretion system
Similarity search - Function
Arc Repressor Mutant, subunit A - #120 / HopA1 effector protein / HopA1 effector protein family / Tir chaperone protein (CesT) family / Tir chaperone protein (CesT) family / Yope Regulator; Chain: A, - #10 / Yope Regulator; Chain: A, / Arc Repressor Mutant, subunit A / Helix non-globular / Special ...Arc Repressor Mutant, subunit A - #120 / HopA1 effector protein / HopA1 effector protein family / Tir chaperone protein (CesT) family / Tir chaperone protein (CesT) family / Yope Regulator; Chain: A, - #10 / Yope Regulator; Chain: A, / Arc Repressor Mutant, subunit A / Helix non-globular / Special / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Type III effector HopA1 / Type III chaperone protein ShcA
Similarity search - Component
Biological speciesPseudomonas syringae pv. tomato (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.56 Å
AuthorsStebbins, C.E. / Janjusevic, R. / Quezada, C.M.
CitationJournal: J.Bacteriol. / Year: 2013
Title: Structure of the HopA1(21-102)-ShcA chaperone-effector complex of Pseudomonas syringae reveals conservation of a virulence factor binding motif from animal to plant pathogens.
Authors: Janjusevic, R. / Quezada, C.M. / Small, J. / Stebbins, C.E.
History
DepositionJul 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type III chaperone protein ShcA
B: Type III effector HopA1


Theoretical massNumber of molelcules
Total (without water)23,1862
Polymers23,1862
Non-polymers00
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-28 kcal/mol
Surface area10920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.832, 67.832, 182.887
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-226-

HOH

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Components

#1: Protein Type III chaperone protein ShcA


Mass: 14462.694 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria)
Strain: DC3000 / Gene: shcA, PSPTO_5353 / References: UniProt: Q87UE6
#2: Protein Type III effector HopA1


Mass: 8722.842 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria)
Strain: DC3000 / Gene: hopA1, PSPTO_5354 / References: UniProt: Q87UE5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.04 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.56→58.74 Å / Num. obs: 34556

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.56→58.74 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.586 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22973 1820 5 %RANDOM
Rwork0.2095 ---
obs0.21051 34556 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.202 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20.22 Å20 Å2
2--0.45 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.56→58.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1549 0 0 116 1665
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191600
X-RAY DIFFRACTIONr_bond_other_d0.0010.021110
X-RAY DIFFRACTIONr_angle_refined_deg1.8581.9812162
X-RAY DIFFRACTIONr_angle_other_deg1.02232711
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0775203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.10724.38473
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00615289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6611512
X-RAY DIFFRACTIONr_chiral_restr0.110.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211791
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02313
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_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.56→1.601 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 101 -
Rwork0.268 2231 -
obs--99.96 %

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