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- PDB-4ynn: Structure of Legionella pneumophila DegQ (S190A variant) -

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Basic information

Entry
Database: PDB / ID: 4ynn
TitleStructure of Legionella pneumophila DegQ (S190A variant)
Components
  • Hepta-peptide
  • Hexa-peptide
  • OctapeptidePeptide
  • Protease DOPeptidase Do
  • UNK-UNK-UNK
KeywordsHYDROLASE / Bacterial Proteins / Legionella / Models / Molecular / Peptide Hydrolases / Protein Conformation
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity / proteolysis
Similarity search - Function
Peptidase M50 / Peptidase family M50 / Peptidase S1C, Do / PDZ domain / PDZ domain 6 / PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / Thrombin, subunit H - #120 / PDZ domain ...Peptidase M50 / Peptidase family M50 / 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 pneumophila subsp. pneumophila (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsWrase, R. / Hilgenfeld, R. / Hansen, G.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationEXC 306 Germany
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Structures of DegQ from Legionella pneumophila Define Distinct ON and OFF States.
Authors: Schubert, A. / Wrase, R. / Hilgenfeld, R. / Hansen, G.
History
DepositionMar 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Aug 26, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease DO
B: Protease DO
C: Protease DO
D: Protease DO
E: Protease DO
F: Protease DO
G: Protease DO
H: Protease DO
I: Octapeptide
J: Hexa-peptide
K: Hepta-peptide
L: Hexa-peptide
M: Hepta-peptide
N: Hepta-peptide
O: Hepta-peptide
P: Hepta-peptide
Q: UNK-UNK-UNK
R: UNK-UNK-UNK
S: UNK-UNK-UNK
T: UNK-UNK-UNK
U: UNK-UNK-UNK
V: UNK-UNK-UNK


Theoretical massNumber of molelcules
Total (without water)387,51422
Polymers387,51422
Non-polymers00
Water0
1
A: Protease DO
D: Protease DO
G: Protease DO
H: Protease DO
I: Octapeptide
L: Hexa-peptide
O: Hepta-peptide
P: Hepta-peptide
Q: UNK-UNK-UNK
T: UNK-UNK-UNK
U: UNK-UNK-UNK
V: UNK-UNK-UNK

A: Protease DO
D: Protease DO
G: Protease DO
H: Protease DO
I: Octapeptide
L: Hexa-peptide
O: Hepta-peptide
P: Hepta-peptide
Q: UNK-UNK-UNK
T: UNK-UNK-UNK
U: UNK-UNK-UNK
V: UNK-UNK-UNK

A: Protease DO
D: Protease DO
G: Protease DO
H: Protease DO
I: Octapeptide
L: Hexa-peptide
O: Hepta-peptide
P: Hepta-peptide
Q: UNK-UNK-UNK
T: UNK-UNK-UNK
U: UNK-UNK-UNK
V: UNK-UNK-UNK


Theoretical massNumber of molelcules
Total (without water)582,21936
Polymers582,21936
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area64090 Å2
ΔGint-375 kcal/mol
Surface area191330 Å2
MethodPISA
2
B: Protease DO
C: Protease DO
E: Protease DO
F: Protease DO
J: Hexa-peptide
K: Hepta-peptide
M: Hepta-peptide
N: Hepta-peptide
R: UNK-UNK-UNK
S: UNK-UNK-UNK

B: Protease DO
C: Protease DO
E: Protease DO
F: Protease DO
J: Hexa-peptide
K: Hepta-peptide
M: Hepta-peptide
N: Hepta-peptide
R: UNK-UNK-UNK
S: UNK-UNK-UNK

B: Protease DO
C: Protease DO
E: Protease DO
F: Protease DO
J: Hexa-peptide
K: Hepta-peptide
M: Hepta-peptide
N: Hepta-peptide
R: UNK-UNK-UNK
S: UNK-UNK-UNK


Theoretical massNumber of molelcules
Total (without water)580,32330
Polymers580,32330
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area61980 Å2
ΔGint-367 kcal/mol
Surface area191430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.909, 147.909, 383.514
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein
Protease DO / Peptidase Do


Mass: 47631.133 Da / Num. of mol.: 8 / Fragment: UNP RESIDUES 31-466 / Mutation: S190A
Source method: isolated from a genetically manipulated source
Details: co-purified peptide fragment modelled as poly-Ala
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: htrA, lpg1331 / Plasmid: pQE-31 / Production host: Escherichia coli (E. coli) / Strain (production host): KU98
References: UniProt: Q5ZVV9, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein/peptide Octapeptide / Peptide


Mass: 698.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: co-purified peptide fragment modelled as poly-Ala / Source: (natural) Escherichia coli (E. coli)
#3: Protein/peptide Hexa-peptide


Mass: 528.644 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: co-purified peptide fragment modelled as poly-Ala / Source: (natural) Escherichia coli (E. coli)
#4: Protein/peptide
Hepta-peptide


Mass: 613.749 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Details: co-purified peptide fragment modelled as poly-Ala / Source: (natural) Escherichia coli (E. coli)
#5: Protein/peptide
UNK-UNK-UNK


Mass: 273.330 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: co-purified peptide fragment modelled as poly-Ala / Source: (natural) Escherichia coli (E. coli)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 100 mM citrate pH5.5; 17.5% (w/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.2→28.543 Å / Num. obs: 77028 / % possible obs: 98.99 % / Redundancy: 7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.5
Reflection shellResolution: 3.2→3.28 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.547 / Mean I/σ(I) obs: 2.1 / % possible all: 94.5

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PV2

3pv2


Resolution: 3.2→28.543 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 21.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2193 3873 5.03 %
Rwork0.181 --
obs0.183 77028 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→28.543 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24195 0 0 0 24195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00424565
X-RAY DIFFRACTIONf_angle_d0.86233270
X-RAY DIFFRACTIONf_dihedral_angle_d14.3389029
X-RAY DIFFRACTIONf_chiral_restr0.0584016
X-RAY DIFFRACTIONf_plane_restr0.0054327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.2390.30161080.28082337X-RAY DIFFRACTION88
3.239-3.27990.30011140.28962447X-RAY DIFFRACTION92
3.2799-3.3230.37351190.29882565X-RAY DIFFRACTION98
3.323-3.36850.29631590.26792646X-RAY DIFFRACTION100
3.3685-3.41650.28521310.24032602X-RAY DIFFRACTION100
3.4165-3.46740.2591340.24282627X-RAY DIFFRACTION100
3.4674-3.52150.29861120.23582686X-RAY DIFFRACTION100
3.5215-3.57910.26051570.21722577X-RAY DIFFRACTION100
3.5791-3.64070.2671350.21492607X-RAY DIFFRACTION100
3.6407-3.70680.24241520.22362668X-RAY DIFFRACTION100
3.7068-3.77790.26721680.23042597X-RAY DIFFRACTION100
3.7779-3.85490.23661190.20892602X-RAY DIFFRACTION100
3.8549-3.93850.26951360.19962647X-RAY DIFFRACTION100
3.9385-4.02990.25921280.20052641X-RAY DIFFRACTION100
4.0299-4.13030.2281330.18342643X-RAY DIFFRACTION100
4.1303-4.24170.21661570.16322620X-RAY DIFFRACTION100
4.2417-4.36610.18081280.15292630X-RAY DIFFRACTION100
4.3661-4.50650.20011530.1452620X-RAY DIFFRACTION100
4.5065-4.66690.18431560.13582609X-RAY DIFFRACTION100
4.6669-4.85290.20841200.14442659X-RAY DIFFRACTION100
4.8529-5.07250.18521450.14092639X-RAY DIFFRACTION100
5.0725-5.33830.15371490.15232627X-RAY DIFFRACTION100
5.3383-5.67040.22581570.17262612X-RAY DIFFRACTION100
5.6704-6.10420.21461250.17122662X-RAY DIFFRACTION100
6.1042-6.71130.19851430.16292656X-RAY DIFFRACTION100
6.7113-7.66590.20351400.17412621X-RAY DIFFRACTION100
7.6659-9.59690.16921490.14172650X-RAY DIFFRACTION100
9.5969-28.54420.17261460.14922658X-RAY DIFFRACTION99

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