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- PDB-4rqy: RE-REFINED STRUCTURE OF 1TE0 - STRUCTURAL ANALYSIS of DEGS, A STR... -

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Basic information

Entry
Database: PDB / ID: 4rqy
TitleRE-REFINED STRUCTURE OF 1TE0 - STRUCTURAL ANALYSIS of DEGS, A STRESS SENSOR OF THE BACTERIAL PERIPLASM
ComponentsProtease degS
KeywordsHYDROLASE / TWO DOMAINS / SERINE PROTEASE / PDZ / ALPHA-BETA PROTEIN / stress response / htra
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
PHOSPHATE ION / : / Serine endoprotease DegS
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / molecular replacement / Resolution: 2.204 Å
AuthorsSauer, R.T. / Grant, R.A.
CitationJournal: Febs Lett. / Year: 2004
Title: Structural analysis of DegS, a stress sensor of the bacterial periplasm.
Authors: Zeth, K.
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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 0THIS ENTRY 4RQY REFLECTS AN ALTERNATIVE MODELING OF THE STRUCTURAL DATA IN R1TE0SF ORIGINAL DATA ...THIS ENTRY 4RQY REFLECTS AN ALTERNATIVE MODELING OF THE STRUCTURAL DATA IN R1TE0SF ORIGINAL DATA DETERMINED BY AUTHOR: K.ZETH

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protease degS
B: Protease degS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8044
Polymers67,6142
Non-polymers1902
Water2,432135
1
A: Protease degS
hetero molecules

A: Protease degS
hetero molecules

A: Protease degS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,9919
Polymers101,4213
Non-polymers5706
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
2
B: Protease degS

B: Protease degS

B: Protease degS


Theoretical massNumber of molelcules
Total (without water)101,4213
Polymers101,4213
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
3
A: Protease degS
hetero molecules
x 12
B: Protease degS
x 12


Theoretical massNumber of molelcules
Total (without water)813,65048
Polymers811,37124
Non-polymers2,27924
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 area83220 Å2
ΔGint-419 kcal/mol
Surface area285350 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

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Components

#1: Protein Protease degS


Mass: 33807.105 Da / Num. of mol.: 2 / 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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.83 Å3/Da / Density % sol: 56.59 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 1TE0

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
PHENIXdev_1760refinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 2.204→28.517 Å / SU ML: 0.22 / σ(F): 1.37 / Phase error: 21.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2195 1927 5.03 %
Rwork0.1819 --
obs0.1838 38289 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.3995 Å2
Refinement stepCycle: LAST / Resolution: 2.204→28.517 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4360 0 10 135 4505
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084416
X-RAY DIFFRACTIONf_angle_d1.0956004
X-RAY DIFFRACTIONf_dihedral_angle_d11.7981616
X-RAY DIFFRACTIONf_chiral_restr0.049733
X-RAY DIFFRACTIONf_plane_restr0.006793
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2036-2.25870.27511180.24432355X-RAY DIFFRACTION90
2.2587-2.31970.27461350.22382591X-RAY DIFFRACTION100
2.3197-2.38790.22591520.20572604X-RAY DIFFRACTION100
2.3879-2.4650.28271420.19642574X-RAY DIFFRACTION100
2.465-2.5530.22251480.19312616X-RAY DIFFRACTION100
2.553-2.65520.24051510.19282580X-RAY DIFFRACTION100
2.6552-2.77590.2711250.19242617X-RAY DIFFRACTION100
2.7759-2.92210.2291310.19922597X-RAY DIFFRACTION100
2.9221-3.1050.26041420.19042613X-RAY DIFFRACTION100
3.105-3.34440.25681320.19192634X-RAY DIFFRACTION100
3.3444-3.68030.2251290.18082620X-RAY DIFFRACTION100
3.6803-4.21140.19311330.172616X-RAY DIFFRACTION100
4.2114-5.30040.17841460.15332651X-RAY DIFFRACTION100
5.3004-28.51920.21461430.18672694X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.5984-0.53730.5791.25480.07811.6252-0.0254-0.113-0.25980.06830.04610.24650.0305-0.2149-0.02310.329-0.00730.0070.2606-0.01420.352433.404860.591854.7807
22.2923-1.6047-0.72421.91111.59142.1342-0.0267-0.20240.3711-0.01640.1569-0.1405-0.13820.1029-0.11680.2754-0.04560.03060.345-0.02190.47639.547135.197133.8372
35.7765-0.0575-0.96165.0205-0.81816.5433-0.00270.7045-0.1607-0.83280.22240.3703-0.0663-0.4821-0.12450.5759-0.0366-0.12750.38790.01670.433730.619481.855826.5318
47.0024-2.64411.30376.0333-1.96285.8978-0.205-1.1766-1.12771.31360.0817-1.66410.49950.91140.07250.86950.1591-0.25020.90350.18771.07435.723717.366964.1972
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq 38:256
2X-RAY DIFFRACTION2chain B and resseq 37:256
3X-RAY DIFFRACTION3chain A and resseq 257:353
4X-RAY DIFFRACTION4chain B and resseq 257:352

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