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- PDB-3pv3: Structure of Legionella fallonii DegQ (S193A variant) -

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Basic information

Entry
Database: PDB / ID: 3pv3
TitleStructure of Legionella fallonii DegQ (S193A variant)
Components
  • DegQ
  • Substrate peptide (Poly-Ala)
KeywordsHYDROLASE / trypsin fold / PDZ domain / chaperone protease
Function / homology
Function and homology information


periplasmic space / serine-type endopeptidase activity / proteolysis
Similarity search - Function
Peptidase S1C, Do / PDZ domain / PDZ domain 6 / PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / Thrombin, subunit H - #120 / PDZ domain / Pdz3 Domain / PDZ domain profile. ...Peptidase S1C, Do / PDZ domain / PDZ domain 6 / PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / Thrombin, subunit H - #120 / PDZ domain / Pdz3 Domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Thrombin, subunit H / Roll / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesLegionella fallonii (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsWrase, R. / Scott, H. / Hilgenfeld, R. / Hansen, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: The Legionella HtrA homologue DegQ is a self-compartmentizing protease that forms large 12-meric assemblies.
Authors: Wrase, R. / Scott, H. / Hilgenfeld, R. / Hansen, G.
History
DepositionDec 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DegQ
B: DegQ
C: DegQ
D: DegQ
E: Substrate peptide (Poly-Ala)
F: Substrate peptide (Poly-Ala)
G: Substrate peptide (Poly-Ala)
H: Substrate peptide (Poly-Ala)


Theoretical massNumber of molelcules
Total (without water)198,9478
Polymers198,9478
Non-polymers00
Water00
1
A: DegQ
B: DegQ
C: DegQ
D: DegQ
E: Substrate peptide (Poly-Ala)
F: Substrate peptide (Poly-Ala)
G: Substrate peptide (Poly-Ala)
H: Substrate peptide (Poly-Ala)

A: DegQ
B: DegQ
C: DegQ
D: DegQ
E: Substrate peptide (Poly-Ala)
F: Substrate peptide (Poly-Ala)
G: Substrate peptide (Poly-Ala)
H: Substrate peptide (Poly-Ala)

A: DegQ
B: DegQ
C: DegQ
D: DegQ
E: Substrate peptide (Poly-Ala)
F: Substrate peptide (Poly-Ala)
G: Substrate peptide (Poly-Ala)
H: Substrate peptide (Poly-Ala)


Theoretical massNumber of molelcules
Total (without water)596,84124
Polymers596,84124
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area49560 Å2
ΔGint-309 kcal/mol
Surface area200710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.030, 155.030, 260.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
DegQ


Mass: 48016.637 Da / Num. of mol.: 4 / Mutation: S193A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella fallonii (bacteria) / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 degP- / References: UniProt: F8W673*PLUS
#2: Protein/peptide
Substrate peptide (Poly-Ala)


Mass: 1720.111 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
Sequence detailsA MIXTURE OF NATURAL OCCURRING PEPTIDE FRAGMENTS WERE FOUND IN THE ACTIVE SITE FOR WHICH THE ...A MIXTURE OF NATURAL OCCURRING PEPTIDE FRAGMENTS WERE FOUND IN THE ACTIVE SITE FOR WHICH THE SEQUENCE IS UNKNOWN.

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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: 3.03 Å3/Da / Density % sol: 59.4 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 22.5% (v/v) PEG 400, 100 mM glycine pH 9.5, vapor diffusion, sitting drop, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: Rayonics MX-225 3x3 CCD / Detector: CCD / Date: Mar 12, 2010
RadiationMonochromator: Double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 3.1→119.351 Å / Num. all: 41803 / Num. obs: 41803 / % possible obs: 98.7 % / Redundancy: 2.9 % / Rsym value: 0.095 / Net I/σ(I): 6.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
3.1-3.272.90.4551.70.455199.4
3.27-3.472.90.2852.70.285199.2
3.47-3.712.90.1913.90.191199.1
3.71-42.90.14350.143198.9
4-4.382.90.1096.30.109198.8
4.38-4.92.90.0927.20.092198.5
4.9-5.662.90.0887.50.088198.3
5.66-6.9330.0956.80.095197.9
6.93-9.830.0629.80.062197.5
9.8-58.6142.90.0538.20.053196.3

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
REFMAC5.5.0110refinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PV2

3pv2


Resolution: 3.1→59.61 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.884 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / ESU R Free: 0.504 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2919 2109 5 %RANDOM
Rwork0.22419 ---
obs0.2277 39691 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.179 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20.14 Å20 Å2
2--0.27 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 3.1→59.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11766 0 0 0 11766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02211909
X-RAY DIFFRACTIONr_bond_other_d00.027898
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.97616131
X-RAY DIFFRACTIONr_angle_other_deg4.432319557
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7951562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.13225.867450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.928152091
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3311550
X-RAY DIFFRACTIONr_chiral_restr0.0890.21961
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02113144
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022038
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5291.57832
X-RAY DIFFRACTIONr_mcbond_other01.53236
X-RAY DIFFRACTIONr_mcangle_it0.977212622
X-RAY DIFFRACTIONr_scbond_it1.02134077
X-RAY DIFFRACTIONr_scangle_it1.8514.53509
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 163 -
Rwork0.287 2913 -
obs--99.29 %

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