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- PDB-1te0: Structural analysis of DegS, a stress sensor of the bacterial per... -

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Basic information

Entry
Database: PDB / ID: 1te0
TitleStructural analysis of DegS, a stress sensor of the bacterial periplasm
ComponentsProtease degS
KeywordsHYDROLASE / two domains / serine protease / PDZ / alpha-beta protein
Function / homology
Function and homology information


: / peptidase Do / cellular response to misfolded protein / serine-type peptidase activity / outer membrane-bounded periplasmic space / peptidase activity / membrane => GO:0016020 / 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 / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain ...Peptidase S1C, DegS / PDZ domain / 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 / Trypsin-like serine proteases / Thrombin, subunit H / Roll / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Serine endoprotease DegS / Serine endoprotease DegS
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRavelli, R.B.G. / Zeth, K.
CitationJournal: FEBS Lett. / Year: 2004
Title: Structural analysis of DegS, a stress sensor of the bacterial periplasm.
Authors: Zeth, K.
History
DepositionMay 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 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.end_auth_comp_id / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protease degS
B: Protease degS


Theoretical massNumber of molelcules
Total (without water)67,3842
Polymers67,3842
Non-polymers00
Water2,936163
1
A: Protease degS

A: Protease degS

A: Protease degS


Theoretical massNumber of molelcules
Total (without water)101,0763
Polymers101,0763
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area6270 Å2
ΔGint-16 kcal/mol
Surface area45350 Å2
MethodPISA, PQS
2
B: Protease degS

B: Protease degS

B: Protease degS


Theoretical massNumber of molelcules
Total (without water)101,0763
Polymers101,0763
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area6290 Å2
ΔGint-16 kcal/mol
Surface area45280 Å2
MethodPISA, PQS
3
A: Protease degS
x 12
B: Protease degS
x 12


Theoretical massNumber of molelcules
Total (without water)808,60924
Polymers808,60924
Non-polymers00
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_656-y+1,z,-x+11
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation12_665-y+1,-z+1,x1
crystal symmetry operation13_555x+1/2,y+1/2,z+1/21
crystal symmetry operation14_555-x+1/2,-y+1/2,z+1/21
crystal symmetry operation15_555-x+1/2,y+1/2,-z+1/21
crystal symmetry operation16_555x+1/2,-y+1/2,-z+1/21
crystal symmetry operation17_555z+1/2,x+1/2,y+1/21
crystal symmetry operation18_555z+1/2,-x+1/2,-y+1/21
crystal symmetry operation19_555-z+1/2,-x+1/2,y+1/21
crystal symmetry operation20_555-z+1/2,x+1/2,-y+1/21
crystal symmetry operation21_555y+1/2,z+1/2,x+1/21
crystal symmetry operation22_555-y+1/2,z+1/2,-x+1/21
crystal symmetry operation23_555y+1/2,-z+1/2,-x+1/21
crystal symmetry operation24_555-y+1/2,-z+1/2,x+1/21
Buried area90690 Å2
ΔGint-223 kcal/mol
Surface area322090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.280, 166.280, 166.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 1 / Auth seq-ID: 37 - 354 / Label seq-ID: 1 - 318

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsThe biological unit of the protein is a trimer. The two subunits within the AU can be transformed into two trimeric oligomers by simple crystallographic symmetry operations.

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Components

#1: Protein Protease degS


Mass: 33692.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: DEGS, HHOB, HTRH, B3235, Z4594, ECS4108 / Plasmid: DegS-TL / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P31137, UniProt: P0AEE3*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.7 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.05 M MgCl2, 0.1 M Hepes, pH 7.5, 30% Polyethylene Glycol Monomethyl ether 550, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 9, 2004 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.2→32 Å / Num. obs: 38296 / % possible obs: 98.6 % / Observed criterion σ(I): 3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.048
Reflection shellHighest resolution: 2.2 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3 / Num. unique all: 38296 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DegP

Resolution: 2.2→32.62 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.901 / SU B: 6.485 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.293 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29526 1927 5 %RANDOM
Rwork0.24459 ---
obs0.24711 36364 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 55.471 Å2
Refinement stepCycle: LAST / Resolution: 2.2→32.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4666 0 0 163 4829
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0224726
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4131.9626442
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.6535636
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.350.2784
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023558
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3490.22087
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2640.2218
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3660.2109
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3970.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.6051.53144
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.63525072
X-RAY DIFFRACTIONr_scbond_it3.89731582
X-RAY DIFFRACTIONr_scangle_it5.6364.51368
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2332 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.190.05
tight thermal0.670.5
LS refinement shellResolution: 2.203→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.336 121
Rwork0.256 2399

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