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- PDB-3pv4: Structure of Legionella fallonii DegQ (Delta-PDZ2 variant) -

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Basic information

Entry
Database: PDB / ID: 3pv4
TitleStructure of Legionella fallonii DegQ (Delta-PDZ2 variant)
ComponentsDegQ
KeywordsHYDROLASE / trypsin fold / PDZ domain / chaperone protease
Function / homology
Function and homology information


serine-type endopeptidase activity
Similarity search - Function
PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain / Pdz3 Domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Trypsin-like serine proteases ...PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain / Pdz3 Domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Trypsin-like serine proteases / 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: 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DegQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6172
Polymers37,5051
Non-polymers1121
Water00
1
A: DegQ
hetero molecules

A: DegQ
hetero molecules

A: DegQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,8516
Polymers112,5143
Non-polymers3373
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 area3900 Å2
ΔGint-39 kcal/mol
Surface area39540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.890, 110.890, 67.933
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: 37504.582 Da / Num. of mol.: 1 / Mutation: Delta(343-439)
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: G1K3R2*PLUS
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd

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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: 2.14 Å3/Da / Density % sol: 42.61 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 23.5% (v/v) PEG 400, 100 mM CdCl2, 100 mM acetate pH 4.5, vapor diffusion, hanging 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: RAYONIX MX-225 / 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→55.46 Å / Num. all: 5626 / Num. obs: 5626 / % possible obs: 99.8 % / Redundancy: 2.6 % / Rsym value: 0.135 / Net I/σ(I): 4.3
Reflection shell

Diffraction-ID: 1 / Redundancy: 2.6 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.1-3.270.4011.821188240.40199.8
3.27-3.470.272.519727600.2799.7
3.47-3.710.2262.818927390.22699.9
3.71-40.1863.217966960.186100
4-4.380.1783.115956120.17899.7
4.38-4.90.1453.814885690.14599.6
4.9-5.660.1413.813315170.14199.8
5.66-6.930.1254.110704040.12599.9
6.93-9.80.095.48563310.0999.6
9.8-55.460.1084.44481740.10899

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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→55.46 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.861 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 32.083 / SU ML: 0.584 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.648 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.32997 258 4.6 %RANDOM
Rwork0.24187 ---
obs0.24584 5367 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 133.82 Å2 / Biso mean: 95.7645 Å2 / Biso min: 70.07 Å2
Baniso -1Baniso -2Baniso -3
1--3.31 Å2-1.66 Å20 Å2
2---3.31 Å20 Å2
3---4.97 Å2
Refinement stepCycle: LAST / Resolution: 3.1→55.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2081 0 1 0 2082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222105
X-RAY DIFFRACTIONr_bond_other_d0.0010.021382
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.9792851
X-RAY DIFFRACTIONr_angle_other_deg0.89833431
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2815277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.91326.05376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.43415375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.217158
X-RAY DIFFRACTIONr_chiral_restr0.0660.2359
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212297
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02355
X-RAY DIFFRACTIONr_mcbond_it0.5361.51388
X-RAY DIFFRACTIONr_mcbond_other0.0491.5576
X-RAY DIFFRACTIONr_mcangle_it0.98522246
X-RAY DIFFRACTIONr_scbond_it0.8393717
X-RAY DIFFRACTIONr_scangle_it1.5074.5604
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 19 -
Rwork0.293 395 -
all-414 -
obs--99.76 %

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