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- PDB-1s28: Crystal Structure of AvrPphF ORF1, the Chaperone for the Type III... -

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Basic information

Entry
Database: PDB / ID: 1s28
TitleCrystal Structure of AvrPphF ORF1, the Chaperone for the Type III Effector AvrPphF ORF2 from P. syringae
ComponentsORF1
KeywordsCHAPERONE / Type III Chaperone
Function / homologyTir chaperone protein (CesT) family / Tir chaperone protein (CesT) family / Yope Regulator; Chain: A, - #10 / Yope Regulator; Chain: A, / protein secretion by the type III secretion system / 2-Layer Sandwich / Alpha Beta / ORF1
Function and homology information
Biological speciesPseudomonas syringae pv. phaseolicola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsSinger, A.U. / Desveaux, D. / Betts, L. / Chang, J.H. / Nimchuk, Z. / Grant, S.R. / Dangl, J.L. / Sondek, J.
CitationJournal: Structure / Year: 2004
Title: Crystal Structures of the Type III Effector Protein AvrPphF and Its Chaperone Reveal Residues Required for Plant Pathogenesis
Authors: Singer, A.U. / Desveaux, D. / Betts, L. / Chang, J.H. / Nimchuk, Z. / Grant, S.R. / Dangl, J.L. / Sondek, J.
History
DepositionJan 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999 sequence The last five residues in C-terminus vary from the published sequence, which authors ... sequence The last five residues in C-terminus vary from the published sequence, which authors believe may have a sequencing error.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ORF1
B: ORF1
C: ORF1
D: ORF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3428
Polymers61,9574
Non-polymers3844
Water00
1
A: ORF1
B: ORF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1714
Polymers30,9792
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-47 kcal/mol
Surface area13100 Å2
MethodPISA
2
C: ORF1
D: ORF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1714
Polymers30,9792
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-48 kcal/mol
Surface area13150 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9710 Å2
ΔGint-120 kcal/mol
Surface area24320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.053, 94.920, 104.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe molecule is a biological dimer, though there were 4 molecules in the asymmetric unit. Molecule 2 can superimpose on molecule 1 with the transformation matrix: -0.985 -0.173 0.003 146.58 -0.173 0.985 -0.016 12.77 0 -0.016 -1.0 3.38

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Components

#1: Protein
ORF1


Mass: 15489.323 Da / Num. of mol.: 4 / Fragment: AvrPphf ORF1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. phaseolicola (bacteria)
Species: Pseudomonas savastanoi / Gene: AvrPphF ORF1 / Plasmid: pProEX-HTa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 RIL Codon Plus / References: UniProt: Q9K2L2
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
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: 3.85 Å3/Da / Density % sol: 67.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Ammonium Sulfate,Tris 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97925, 0.97936, 0.97167
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 23, 2003 / Details: vertically focussing mirror
RadiationMonochromator: Double Crystal Monochromater Si-220 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979251
20.979361
30.971671
ReflectionResolution: 3→20 Å / Num. all: 18977 / Num. obs: 18973 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 72.7 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 26.9
Reflection shellResolution: 3→3.11 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 7.66 / Num. unique all: 1851 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 3→19.97 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1713413.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.29 893 4.8 %RANDOM
Rwork0.248 ---
all0.251 19093 --
obs0.248 18470 97.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.280684 e/Å3
Displacement parametersBiso mean: 43.2 Å2
Baniso -1Baniso -2Baniso -3
1-11.54 Å20 Å20 Å2
2---9.79 Å20 Å2
3----1.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.38 Å
Luzzati d res low-4 Å
Luzzati sigma a0.25 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 3→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4252 0 20 0 4272
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d1.37
X-RAY DIFFRACTIONc_mcbond_it7.831.5
X-RAY DIFFRACTIONc_mcangle_it12.432
X-RAY DIFFRACTIONc_scbond_it11.912
X-RAY DIFFRACTIONc_scangle_it17.542.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.338 144 4.9 %
Rwork0.298 2811 -
obs--94.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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