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- PDB-4rr1: re-refinement of entry 1sot, Crystal Structure of the DegS stress... -

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Basic information

Entry
Database: PDB / ID: 4rr1
Titlere-refinement of entry 1sot, Crystal Structure of the DegS stress sensor
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
NICKEL (II) ION / PHOSPHATE ION / : / Serine endoprotease DegS
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.3 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
Remark 0THIS ENTRY 4RR1 REFLECTS AN ALTERNATIVE MODELING OF THE STRUCTURAL DATA IN R1SOTSF ORIGINAL DATA ...THIS ENTRY 4RR1 REFLECTS AN ALTERNATIVE MODELING OF THE STRUCTURAL DATA IN R1SOTSF 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,2155
Polymers103,0623
Non-polymers1542
Water8,053447
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-39 kcal/mol
Surface area35610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.680, 143.060, 41.530
Angle α, β, γ (deg.)90.000, 90.070, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protease degS


Mass: 34353.898 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: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 447 / 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: 2.99 Å3/Da / Density % sol: 58.9 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 1SOT.

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameVersionClassificationNB
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 2.3→14.996 Å / SU ML: 0.23 / σ(F): 1.35 / Phase error: 22.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2172 2616 5.07 %random
Rwork0.1839 ---
obs0.1856 51616 96.44 %-
all-53521 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 282.75 Å2 / Biso mean: 66.6488 Å2 / Biso min: 16.08 Å2
Refinement stepCycle: LAST / Resolution: 2.3→14.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6039 0 6 447 6492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056138
X-RAY DIFFRACTIONf_angle_d0.9358355
X-RAY DIFFRACTIONf_chiral_restr0.0361041
X-RAY DIFFRACTIONf_plane_restr0.0051088
X-RAY DIFFRACTIONf_dihedral_angle_d10.4582229
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.34170.26711360.23662620275699
2.3417-2.38650.24731460.212626202766100
2.3865-2.43510.28111430.209927282871100
2.4351-2.48780.23271290.212326082737100
2.4878-2.54540.24521490.206426362785100
2.5454-2.60870.25191530.213527242877100
2.6087-2.67890.24251330.212556268998
2.6789-2.75720.24611380.20722676281498
2.7572-2.84560.25191570.205426142771100
2.8456-2.94660.23431330.18832677281099
2.9466-3.06360.22451490.19242625277499
3.0636-3.20180.22031470.18442671281899
3.2018-3.36880.23291260.18672631275799
3.3688-3.57710.21131420.18182528267095
3.5771-3.8490.2361250.18052285241085
3.849-4.22850.18211020.16282557265994
4.2285-4.82240.14791370.14162496263394
4.8224-6.010.22171310.18172504263592
6.01-14.99620.21161400.18952244238483
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)
10.9754-0.3685-0.14711.10690.08360.47690.0284-0.1298-0.10540.0383-0.0114-0.2428-0.01120.0491-0.01620.25280.0108-0.03580.26350.02930.172935.633819.64492.8204
21.45710.0363-0.02151.9694-0.28681.5356-0.0045-0.1852-1.45370.21760.1112-0.03791.44210.2935-0.09431.22330.0698-0.03790.5960.08681.674311.7357-15.14385.9712
31.77330.0323-0.3231.39420.83970.79270.2239-0.36980.20231.0177-0.33231.59430.2536-1.03960.11640.7547-0.14670.35650.9068-0.14591.232124.275857.739316.1569
42.18350.27840.56312.28330.27710.8046-0.2911-0.40550.46230.1051-0.1317-1.5782-0.50050.72530.42180.825-0.1447-0.03651.0523-0.11721.968477.512912.3108-1.7327
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A or chain B or chain C) and resseq 42:256A0
2X-RAY DIFFRACTION2chain A and resseq 257:361A257 - 361
3X-RAY DIFFRACTION3chain B and resseq 257:361B257 - 361
4X-RAY DIFFRACTION4chain C and resseq 257:361C257 - 361

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