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- PDB-3ph0: Crystal structure of the heteromolecular chaperone, AscE-AscG, fr... -

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Basic information

Entry
Database: PDB / ID: 3ph0
TitleCrystal structure of the heteromolecular chaperone, AscE-AscG, from the type III secretion system in Aeromonas hydrophila
Components
  • AscE
  • AscG
KeywordsCHAPERONE / Type III secretion system / chaperones AscE and AscG
Function / homology
Function and homology information


Type III secretion system YscG / Bacterial type III secretion system chaperone protein / Type III secretion system, secretion protein E / Type III secretion system, cytoplasmic E component of needle / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #1040 / Immunoglobulin FC, subunit C / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily ...Type III secretion system YscG / Bacterial type III secretion system chaperone protein / Type III secretion system, secretion protein E / Type III secretion system, cytoplasmic E component of needle / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #1040 / Immunoglobulin FC, subunit C / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesAeromonas hydrophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsChatterjee, C. / Kumar, S. / Chakraborty, S. / Tan, Y.W. / Leung, K.Y. / Sivaraman, J. / Mok, Y.K.
CitationJournal: Plos One / Year: 2011
Title: Crystal structure of the heteromolecular chaperone, AscE-AscG, from the type III secretion system in Aeromonas hydrophila
Authors: Chatterjee, C. / Kumar, S. / Chakraborty, S. / Tan, Y.W. / Leung, K.Y. / Sivaraman, J. / Mok, Y.K.
History
DepositionNov 3, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: AscE
C: AscG
B: AscE
D: AscG


Theoretical massNumber of molelcules
Total (without water)28,6674
Polymers28,6674
Non-polymers00
Water4,197233
1
A: AscE
C: AscG


Theoretical massNumber of molelcules
Total (without water)14,3332
Polymers14,3332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-16 kcal/mol
Surface area6560 Å2
MethodPISA
2
B: AscE
D: AscG


Theoretical massNumber of molelcules
Total (without water)14,3332
Polymers14,3332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-15 kcal/mol
Surface area6690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.159, 71.937, 86.735
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein AscE


Mass: 7572.576 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q1EHA4
#2: Protein AscG


Mass: 6760.776 Da / Num. of mol.: 2 / Fragment: residues 1-61
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q1EHA2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 47.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10mM Tris(pH 7.4), 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9792, 0.9794, 0.9640, 1.542
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 1, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97941
30.9641
41.5421
ReflectionResolution: 2.4→50 Å / Num. obs: 16865 / % possible obs: 99.8 % / Rsym value: 0.089
Reflection shellHighest resolution: 2.4 Å / Rsym value: 0.089 / % possible all: 99.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
RESOLVEphasing
CNSrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MAD / Resolution: 2.4→20 Å / Occupancy max: 1 / Occupancy min: 1
RfactorNum. reflection% reflection
Rfree0.2923 1601 7.9 %
Rwork0.239 --
obs-11163 82.9 %
Solvent computationBsol: 51.8285 Å2
Displacement parametersBiso max: 105.82 Å2 / Biso mean: 44.3555 Å2 / Biso min: 20.74 Å2
Baniso -1Baniso -2Baniso -3
1--12.993 Å20 Å20 Å2
2--2.061 Å20 Å2
3---10.931 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1745 0 0 233 1978
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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