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- PDB-3lh3: DFP modified DegS delta PDZ -

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Basic information

Entry
Database: PDB / ID: 3lh3
TitleDFP modified DegS delta PDZ
ComponentsProtease degS
KeywordsHYDROLASE / protease / stress-sensor / HtrA / PDZ OMP / Serine protease
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 profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Trypsin / Trypsin-like serine proteases ...Peptidase S1C, DegS / PDZ domain / Peptidase S1C / Trypsin-like peptidase 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsSohn, J. / Grant, R.A. / Sauer, R.T.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Allostery is an intrinsic property of the protease domain of DegS: implications for enzyme function and evolution.
Authors: Sohn, J. / Grant, R.A. / Sauer, R.T.
History
DepositionJan 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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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: Protease degS
E: Protease degS
F: Protease degS
G: Protease degS
H: Protease degS
I: Protease degS


Theoretical massNumber of molelcules
Total (without water)234,1109
Polymers234,1109
Non-polymers00
Water13,259736
1
A: Protease degS
B: Protease degS
C: Protease degS


Theoretical massNumber of molelcules
Total (without water)78,0373
Polymers78,0373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-21 kcal/mol
Surface area25940 Å2
MethodPISA
2
D: Protease degS
E: Protease degS
F: Protease degS


Theoretical massNumber of molelcules
Total (without water)78,0373
Polymers78,0373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-20 kcal/mol
Surface area25240 Å2
MethodPISA
3
G: Protease degS
H: Protease degS
I: Protease degS


Theoretical massNumber of molelcules
Total (without water)78,0373
Polymers78,0373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6860 Å2
ΔGint-21 kcal/mol
Surface area23620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.531, 132.745, 231.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Protease degS


Mass: 26012.234 Da / Num. of mol.: 9 / Fragment: protease domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b3235, degS, hhoB, htrH, JW3204 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): X90(DE3)
References: UniProt: P0AEE3, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 736 / 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: 2.34 Å3/Da / Density % sol: 47.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50 MM NA CACODYLATE, 100 MM NA CITRATE, 20% ISOPROPANOL, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.347→50 Å / Num. obs: 90170 / % possible obs: 97.6 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2.347-2.435.50.40197.2
2.43-2.5360.3198
2.53-2.656.40.23897.9
2.65-2.796.50.18498.5
2.79-2.966.50.12698
2.96-3.196.50.08798.3
3.19-3.516.50.07198.5
3.51-4.025.50.07790.3
4.02-5.066.80.05199.7
5.06-507.30.03399.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→37.14 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.31 / σ(F): 1 / Phase error: 22.35 / Stereochemistry target values: ML
Details: TO OBTAIN THE BEST POSSIBLE GEOMETRY, THIS STRUCTURE WAS REFINED WITH HYDROGENS WHOSE COORDINATES WERE DETERMINED BY THE ATTACHED HEAVY ATOM. AUTHORS STATE THAT ALTHOUGH HYDROGENS CANNOT BE ...Details: TO OBTAIN THE BEST POSSIBLE GEOMETRY, THIS STRUCTURE WAS REFINED WITH HYDROGENS WHOSE COORDINATES WERE DETERMINED BY THE ATTACHED HEAVY ATOM. AUTHORS STATE THAT ALTHOUGH HYDROGENS CANNOT BE VISUALIZED AT THIS RESOLUTION, THEY ARE PRESENT AND CONTRIBUTE TO SCATTERING. THE HYDROGENS ARE KEPT IN THIS ENTRY BECAUSE INDEPENDENT ASSESSMENT OF MANY ASPECTS OF THE GEOMETRY, INCLUDING STERIC CLASHES, REQUIRE THEIR PRESENCE. MOREOVER, REMOVING HYDROGEN ATOMS AFTER REFINEMENT MAKES INDEPENDENT ASSESSMENT OF REFINEMENT STATISTICS EFFECTIVELY IRREPRODUCIBLE.
RfactorNum. reflection% reflection
Rfree0.227 4123 4.88 %
Rwork0.185 --
obs0.187 84470 91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.68 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 49.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.941 Å20 Å2-0 Å2
2--0.649 Å20 Å2
3----1.589 Å2
Refinement stepCycle: LAST / Resolution: 2.35→37.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13889 0 0 736 14625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00414061
X-RAY DIFFRACTIONf_angle_d0.88319117
X-RAY DIFFRACTIONf_dihedral_angle_d17.6015092
X-RAY DIFFRACTIONf_chiral_restr0.052306
X-RAY DIFFRACTIONf_plane_restr0.0042515
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.37480.26871110.20511935X-RAY DIFFRACTION64
2.3748-2.40380.25091250.19662500X-RAY DIFFRACTION83
2.4038-2.43420.25521260.2042561X-RAY DIFFRACTION86
2.4342-2.46620.25281280.20052568X-RAY DIFFRACTION84
2.4662-2.50.26711530.19732617X-RAY DIFFRACTION88
2.5-2.53570.28131420.19112641X-RAY DIFFRACTION88
2.5357-2.57360.28341430.19842667X-RAY DIFFRACTION89
2.5736-2.61380.2291470.1952715X-RAY DIFFRACTION91
2.6138-2.65660.32161360.20812743X-RAY DIFFRACTION90
2.6566-2.70240.271330.1882754X-RAY DIFFRACTION92
2.7024-2.75150.26041470.1972758X-RAY DIFFRACTION90
2.7515-2.80440.26811510.19912775X-RAY DIFFRACTION93
2.8044-2.86170.20911370.18622778X-RAY DIFFRACTION92
2.8617-2.92390.27431560.18252833X-RAY DIFFRACTION95
2.9239-2.99190.23671590.18492803X-RAY DIFFRACTION93
2.9919-3.06660.21991420.18062873X-RAY DIFFRACTION95
3.0666-3.14950.21981380.18092877X-RAY DIFFRACTION94
3.1495-3.24210.25441580.19392869X-RAY DIFFRACTION95
3.2421-3.34670.25881530.18762866X-RAY DIFFRACTION95
3.3467-3.46630.22051390.17762867X-RAY DIFFRACTION94
3.4663-3.60490.2191090.18432371X-RAY DIFFRACTION77
3.6049-3.76880.28381140.19472640X-RAY DIFFRACTION86
3.7688-3.96730.19881170.17772904X-RAY DIFFRACTION94
3.9673-4.21560.17611440.15552957X-RAY DIFFRACTION97
4.2156-4.54050.17311650.13543043X-RAY DIFFRACTION99
4.5405-4.99650.17151530.14013029X-RAY DIFFRACTION99
4.9965-5.71720.17571640.16023069X-RAY DIFFRACTION99
5.7172-7.19450.22451660.19533133X-RAY DIFFRACTION99
7.1945-37.14640.21241670.21053201X-RAY DIFFRACTION98

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