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- PDB-4rqz: re-refinement of 1soz, Crystal Structure of DegS protease in comp... -

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Basic information

Entry
Database: PDB / ID: 4rqz
Titlere-refinement of 1soz, Crystal Structure of DegS protease in complex with an activating peptide
Components
  • Protease degS
  • activating peptide
KeywordsHydrolase/peptide / STRESS RESPONSE / PROTEIN QUALITY CONTROL / PDZ / UPR / HTRA / Hydrolase / Hydrolase-peptide complex
Function / homology
Function and homology information


peptidase Do / cellular response to misfolded protein / protein quality control for misfolded or incompletely synthesized proteins / serine-type peptidase activity / peptidase activity / outer membrane-bounded periplasmic space / serine-type endopeptidase activity / proteolysis / identical protein binding / plasma membrane
Similarity search - Function
Peptidase S1C, DegS / PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Trypsin ...Peptidase S1C, DegS / PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
: / Serine endoprotease DegS
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsSauer, R.T. / Grant, R.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2004
Title: Crystal structure of the DegS stress sensor: How a PDZ domain recognizes misfolded protein and activates a protease.
Authors: Wilken, C. / Kitzing, K. / Kurzbauer, R. / Ehrmann, M. / Clausen, T.
History
DepositionNov 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2Feb 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
Remark 0THIS ENTRY 4RQZ REFLECTS AN ALTERNATIVE MODELING OF THE STRUCTURAL DATA IN R1SOZSF ORIGINAL DATA ...THIS ENTRY 4RQZ REFLECTS AN ALTERNATIVE MODELING OF THE STRUCTURAL DATA IN R1SOZSF ORIGINAL DATA DETERMINED BY AUTHOR: C.WILKEN,K.KITZING,R.KURZBAUER,M.EHRMANN,T.CLAUSEN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease degS
B: Protease degS
C: Protease degS
D: activating peptide
E: activating peptide
F: activating peptide


Theoretical massNumber of molelcules
Total (without water)103,4076
Polymers103,4076
Non-polymers00
Water4,594255
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)205.984, 142.710, 41.167
Angle α, β, γ (deg.)90.000, 89.240, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protease degS


Mass: 33243.664 Da / Num. of mol.: 3 / Fragment: protease and pdz domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: degS, P12B_c3347 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: H9UXC8, UniProt: P0AEE3*PLUS
#2: Protein/peptide activating peptide


Mass: 1225.374 Da / Num. of mol.: 3 / Fragment: synthetic activating peptide / Source method: obtained synthetically / Details: synthetic peptide
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.93 Å3/Da / Density % sol: 57.95 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 1SOZ.

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameVersionClassificationNB
PHENIXdev_1760refinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 2.4→14.94 Å / SU ML: 0.3 / σ(F): 1.35 / Phase error: 26.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2264 2135 5.08 %random
Rwork0.1959 ---
all0.1975 46223 --
obs0.1975 42017 90.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 245.74 Å2 / Biso mean: 95.9271 Å2 / Biso min: 29.22 Å2
Refinement stepCycle: LAST / Resolution: 2.4→14.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5992 0 0 255 6247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016069
X-RAY DIFFRACTIONf_angle_d1.1088265
X-RAY DIFFRACTIONf_chiral_restr0.0441023
X-RAY DIFFRACTIONf_plane_restr0.0061083
X-RAY DIFFRACTIONf_dihedral_angle_d11.5772156
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.45560.32881270.3162387251482
2.4556-2.51670.35191480.29032751289996
2.5167-2.58450.31531580.26442852301096
2.5845-2.66010.3311290.26762762289195
2.6601-2.74540.32091500.25832812296295
2.7454-2.84290.26171620.2492756291897
2.8429-2.95590.24971330.21292873300697
2.9559-3.08930.24081660.19432799296597
3.0893-3.25060.22821590.19152794295395
3.2506-3.45190.21491350.18832674280991
3.4519-3.71460.25571450.19492654279991
3.7146-4.08150.2251270.19512504263185
4.0815-4.65640.19411270.15772378250581
4.6564-5.80870.18891380.17822432257083
5.8087-14.93990.1921310.18062454258583

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