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- PDB-3ou0: re-refined 3CS0 -

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Basic information

Entry
Database: PDB / ID: 3ou0
Titlere-refined 3CS0
Components
  • Periplasmic serine endoprotease DegP
  • heptapeptide
  • pentapeptide
KeywordsHYDROLASE / protease
Function / homology
Function and homology information


peptidase Do / response to temperature stimulus / protein quality control for misfolded or incompletely synthesized proteins / : / serine-type peptidase activity / protein folding / peptidase activity / outer membrane-bounded periplasmic space / response to heat / response to oxidative stress ...peptidase Do / response to temperature stimulus / protein quality control for misfolded or incompletely synthesized proteins / : / serine-type peptidase activity / protein folding / peptidase activity / outer membrane-bounded periplasmic space / response to heat / response to oxidative stress / periplasmic space / serine-type endopeptidase activity / proteolysis / identical protein binding / plasma membrane
Similarity search - Function
Peptidase S1C, Do / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily ...Peptidase S1C, Do / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Trypsin-like serine proteases / Thrombin, subunit H / Roll / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Periplasmic serine endoprotease DegP
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SAD / Resolution: 3 Å
AuthorsSauer, R.T. / Grant, R.A. / Kim, S.
CitationJournal: Nature / Year: 2008
Title: Structural basis for the regulated protease and chaperone function of DegP.
Authors: Tobias Krojer / Justyna Sawa / Eva Schäfer / Helen R Saibil / Michael Ehrmann / Tim Clausen /
Abstract: All organisms have to monitor the folding state of cellular proteins precisely. The heat-shock protein DegP is a protein quality control factor in the bacterial envelope that is involved in ...All organisms have to monitor the folding state of cellular proteins precisely. The heat-shock protein DegP is a protein quality control factor in the bacterial envelope that is involved in eliminating misfolded proteins and in the biogenesis of outer-membrane proteins. Here we describe the molecular mechanisms underlying the regulated protease and chaperone function of DegP from Escherichia coli. We show that binding of misfolded proteins transforms hexameric DegP into large, catalytically active 12-meric and 24-meric multimers. A structural analysis of these particles revealed that DegP represents a protein packaging device whose central compartment is adaptable to the size and concentration of substrate. Moreover, the inner cavity serves antagonistic functions. Whereas the encapsulation of folded protomers of outer-membrane proteins is protective and might allow safe transit through the periplasm, misfolded proteins are eliminated in the molecular reaction chamber. Oligomer reassembly and concomitant activation on substrate binding may also be critical in regulating other HtrA proteases implicated in protein-folding diseases.
History
DepositionSep 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 12, 2011Group: Other
Revision 1.3Feb 22, 2012Group: Other
Revision 1.4Nov 6, 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
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
Remark 0THIS ENTRY 3OU0 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA R3CS0SF DETERMINED ...THIS ENTRY 3OU0 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA R3CS0SF DETERMINED BY AUTHORS OF THE PDB ENTRY 3CS0: T.KROJER,J.SAWA,E.SCHAEFER,H.R.SAIBIL,M.EHRMANN,T.CLAUSEN
Remark 200AUTHOR USED THE SF(MR) DATA FROM ENTRY 3CS0
Remark 999THIS ENTRY 3OU0 REFLECTS AN ALTERNATIVE MODELING OF X-RAY DATA R3CS0SF. 3OU0 HAS AN EXTRA CHAIN C ...THIS ENTRY 3OU0 REFLECTS AN ALTERNATIVE MODELING OF X-RAY DATA R3CS0SF. 3OU0 HAS AN EXTRA CHAIN C COMPARING THE ORIGINAL DEPOSITION 3CS0.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Periplasmic serine endoprotease DegP
B: pentapeptide
C: heptapeptide


Theoretical massNumber of molelcules
Total (without water)48,5673
Polymers48,5673
Non-polymers00
Water00
1
A: Periplasmic serine endoprotease DegP
x 24


Theoretical massNumber of molelcules
Total (without water)1,140,22724
Polymers1,140,22724
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_555-y,-x,-z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation19_555-x,-z,-y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_555-z,-y,-x1
Buried area75920 Å2
ΔGint-457 kcal/mol
Surface area364800 Å2
MethodPISA
2
B: pentapeptide


  • defined by author&software
  • 444 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)4441
Polymers4441
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: heptapeptide


  • defined by author&software
  • 614 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)6141
Polymers6141
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)253.929, 253.929, 253.929
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432

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Components

#1: Protein Periplasmic serine endoprotease DegP / PROTEASE DO / DEGP


Mass: 47509.449 Da / Num. of mol.: 1 / Fragment: DegP, UNP residues 27-474
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: b0161, degP, htrA, JW0157, ptd / Production host: Escherichia coli (E. coli)
References: UniProt: P0C0V0, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein/peptide pentapeptide


Mass: 443.539 Da / Num. of mol.: 1 / Source method: obtained synthetically / Production host: Escherichia coli (E. coli)
#3: Protein/peptide heptapeptide


Mass: 613.749 Da / Num. of mol.: 1 / Source method: obtained synthetically
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: 3.51 Å3/Da / Density % sol: 64.97 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.2_432refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 3→14.963 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8461 / SU ML: 0.33 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2286 708 4.97 %random
Rwork0.1955 ---
all0.1972 14253 --
obs0.1972 14253 98.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.181 Å2 / ksol: 0.302 e/Å3
Displacement parametersBiso max: 218.7 Å2 / Biso mean: 74.1252 Å2 / Biso min: 13.04 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3→14.963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2877 0 0 0 2877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032901
X-RAY DIFFRACTIONf_angle_d0.6733927
X-RAY DIFFRACTIONf_chiral_restr0.046479
X-RAY DIFFRACTIONf_plane_restr0.003520
X-RAY DIFFRACTIONf_dihedral_angle_d12.0281048
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0003-3.22980.33111270.28872558268596
3.2298-3.55090.26271370.22132655279298
3.5509-4.05580.21341500.1822689283999
4.0558-5.07640.17851450.153527452890100
5.0764-14.96310.24141490.203128983047100

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