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- PDB-3pv5: Structure of Legionella fallonii DegQ (N189G/P190G variant) -

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Basic information

Entry
Database: PDB / ID: 3pv5
TitleStructure of Legionella fallonii DegQ (N189G/P190G variant)
ComponentsDegQ
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Sep 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

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Assembly

Deposited unit
A: DegQ
B: DegQ
C: DegQ
D: DegQ


Theoretical massNumber of molelcules
Total (without water)191,7424
Polymers191,7424
Non-polymers00
Water2,936163
1
A: DegQ
B: DegQ
C: DegQ
D: DegQ

A: DegQ
B: DegQ
C: DegQ
D: DegQ

A: DegQ
B: DegQ
C: DegQ
D: DegQ


Theoretical massNumber of molelcules
Total (without water)575,22612
Polymers575,22612
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area46920 Å2
ΔGint-230 kcal/mol
Surface area191020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.110, 137.110, 326.911
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
DegQ


Mass: 47935.523 Da / Num. of mol.: 4 / Mutation: N189G, P190G
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): K-12 degP- mutation / References: UniProt: F8W674*PLUS
#2: Water ChemComp-HOH / 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: 3.08 Å3/Da / Density % sol: 60.12 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 32% (v/v) PEG 400, 100 mM MES pH 6.5, vapor diffusion, sitting drop, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 19, 2009
RadiationMonochromator: Double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→111.61 Å / Num. all: 89543 / Num. obs: 89543 / % possible obs: 99.9 % / Redundancy: 5.4 % / Rsym value: 0.066 / Net I/σ(I): 14.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.4-2.5350.5691.465692130940.56999.9
2.53-2.685.10.3562.263218123870.35699.9
2.68-2.875.20.2263.460780115940.226100
2.87-3.15.40.145.458657108120.14100
3.1-3.395.60.0878.25631099790.087100
3.39-3.795.80.05911.55175989840.059100
3.79-4.385.80.0512.64618279820.05100
4.38-5.375.80.05311.53902767290.053100
5.37-7.595.80.04414.13005151650.044100
7.59-43.9535.60.027221585628170.02799.1

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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: 2.4→44.46 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.906 / Occupancy max: 1 / Occupancy min: 1 / SU B: 8.178 / SU ML: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.31 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2846 4493 5 %RANDOM
Rwork0.2311 ---
obs0.23379 89543 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 93.96 Å2 / Biso mean: 44.712 Å2 / Biso min: 16.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.4→44.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11448 0 0 163 11611
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.02211588
X-RAY DIFFRACTIONr_bond_other_d0.0010.027716
X-RAY DIFFRACTIONr_angle_refined_deg1.8511.97715688
X-RAY DIFFRACTIONr_angle_other_deg1.039319105
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.31851519
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.27725.885435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.118152062
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0811547
X-RAY DIFFRACTIONr_chiral_restr0.1160.21910
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02112767
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021988
X-RAY DIFFRACTIONr_mcbond_it1.1311.57590
X-RAY DIFFRACTIONr_mcbond_other0.2081.53163
X-RAY DIFFRACTIONr_mcangle_it2.116212255
X-RAY DIFFRACTIONr_scbond_it2.87533998
X-RAY DIFFRACTIONr_scangle_it4.764.53433
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 332 -
Rwork0.362 6270 -
all-6602 -
obs--99.89 %

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