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- PDB-4rr0: re-refined 1vcw, CRYSTAL STRUCTURE OF DEGS AFTER BACKSOAKING THE ... -

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Basic information

Entry
Database: PDB / ID: 4rr0
Titlere-refined 1vcw, CRYSTAL STRUCTURE OF DEGS AFTER BACKSOAKING THE ACTIVATING PEPTIDE
ComponentsProtease degS
KeywordsHYDROLASE / STRESS RESPONSE / PROTEIN QUALITY CONTROL / PDZ / UPR / HTRA
Function / homology
Function and homology information


peptidase Do / cellular response to misfolded protein / serine-type peptidase activity / outer membrane-bounded periplasmic space / peptidase activity / 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: 3.054 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details
Remark 0THIS ENTRY 4RR0 REFLECTS AN ALTERNATIVE MODELING OF THE STRUCTURAL DATA IN R1VCWSF ORIGINAL DATA ...THIS ENTRY 4RR0 REFLECTS AN ALTERNATIVE MODELING OF THE STRUCTURAL DATA IN R1VCWSF 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

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Assembly

Deposited unit
A: Protease degS
B: Protease degS
C: Protease degS


Theoretical massNumber of molelcules
Total (without water)99,7313
Polymers99,7313
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-26 kcal/mol
Surface area35360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)206.990, 142.733, 41.231
Angle α, β, γ (deg.)90.000, 90.090, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 42 - 353 / Label seq-ID: 1 - 312

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC

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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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.05 Å3/Da / Density % sol: 59.72 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 1VCW.

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameVersionClassificationNB
PHENIX(phenix.refine: dev_1760)refinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 3.054→19.902 Å / SU ML: 0.48 / σ(F): 1.36 / Phase error: 27.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2563 1104 5.05 %random
Rwork0.2259 ---
all0.2274 21866 --
obs0.2274 21866 96.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 292.86 Å2 / Biso mean: 102.6778 Å2 / Biso min: 19.44 Å2
Refinement stepCycle: LAST / Resolution: 3.054→19.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6018 0 0 3 6021
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046088
X-RAY DIFFRACTIONf_angle_d0.8798293
X-RAY DIFFRACTIONf_chiral_restr0.0331026
X-RAY DIFFRACTIONf_plane_restr0.0041091
X-RAY DIFFRACTIONf_dihedral_angle_d11.8682215
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4542X-RAY DIFFRACTION9.403TORSIONAL
12B4542X-RAY DIFFRACTION9.403TORSIONAL
13C4542X-RAY DIFFRACTION9.403TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0542-3.19270.39591510.34112540269195
3.1927-3.36030.31841510.29482595274698
3.3603-3.56970.25571290.25972633276298
3.5697-3.84350.26541340.25172638277298
3.8435-4.22690.26441380.22622596273497
4.2269-4.83090.21131270.18122625275297
4.8309-6.05780.24771430.2142579272296
6.0578-19.90290.22711310.1952556268793

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