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- PDB-1ky9: Crystal Structure of DegP (HtrA) -

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Basic information

Entry
Database: PDB / ID: 1ky9
TitleCrystal Structure of DegP (HtrA)
ComponentsPROTEASE DO
KeywordsHYDROLASE / protein quality control / serine protease / trypsin / chaperone / PDZ / ATP-independent / temperature-regulated / periplasm / cage-forming protein
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 / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsKrojer, T. / Garrido-Franco, M. / Huber, R. / Ehrmann, M. / Clausen, T.
CitationJournal: Nature / Year: 2002
Title: Crystal structure of DegP (HtrA) reveals a new protease-chaperone machine.
Authors: Krojer, T. / Garrido-Franco, M. / Huber, R. / Ehrmann, M. / Clausen, T.
History
DepositionFeb 4, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEASE DO
B: PROTEASE DO


Theoretical massNumber of molelcules
Total (without water)95,0192
Polymers95,0192
Non-polymers00
Water2,990166
1
A: PROTEASE DO
x 6


Theoretical massNumber of molelcules
Total (without water)285,0576
Polymers285,0576
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
2
B: PROTEASE DO
x 6


Theoretical massNumber of molelcules
Total (without water)285,0576
Polymers285,0576
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation9_555-x,-x+y,-z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)121.374, 121.374, 233.667
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
DetailsHexamers of molecule A and B are entirely formed by crystal symmetry.

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Components

#1: Protein PROTEASE DO / DegP / HTRA


Mass: 47509.449 Da / Num. of mol.: 2 / Mutation: S210A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: degP / Production host: Escherichia coli (E. coli)
References: UniProt: P0C0V0, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O
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: 2.61 Å3/Da / Density % sol: 52.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Isopropanol, PEG 2000 MME, Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 %isopropanol1reservoir
210 %PEG2000 MME1reservoir
30.1 MTris-HCl1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9500, 0.9795, 0.9797
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 22, 2001
RadiationMonochromator: Si111 or Si311 crystals, LN2 cooled / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.951
20.97951
30.97971
ReflectionResolution: 2.8→20 Å / Num. all: 48422 / Num. obs: 48312 / % possible obs: 97 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 82 Å2 / Rsym value: 0.083
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 4397 / Rsym value: 0.469 / % possible all: 92.2
Reflection
*PLUS
Lowest resolution: 20 Å / Rmerge(I) obs: 0.083
Reflection shell
*PLUS
% possible obs: 92.2 % / Rmerge(I) obs: 0.469

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Processing

Software
NameClassification
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.275 2338 RANDOM
Rwork0.218 --
all0.229 47278 -
obs0.226 47131 -
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5200 0 0 166 5366
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.8
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor all: 0.229 / Rfactor obs: 0.218 / Rfactor Rfree: 0.275 / Rfactor Rwork: 0.218
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 2

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