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- PDB-4yo1: Structure of Legionella pneumophila DegQ (delta PDZ2 variant) -

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Basic information

Entry
Database: PDB / ID: 4yo1
TitleStructure of Legionella pneumophila DegQ (delta PDZ2 variant)
ComponentsDegQ
KeywordsHYDROLASE / Bacterial Proteins / Legionella / Models / Molecular / Peptide Hydrolases / Protein Conformation / chaperone
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 / PDZ domain / Pdz3 Domain ...Peptidase M50 / Peptidase family M50 / Peptidase S1C, Do / PDZ domain / PDZ domain 6 / 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 pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWrase, R. / Hilgenfeld, R. / Hansen, G.
Funding support Germany, 1items
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 11, 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 ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DegQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7466
Polymers37,1841
Non-polymers5625
Water0
1
A: DegQ
hetero molecules

A: DegQ
hetero molecules

A: DegQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,23918
Polymers111,5523
Non-polymers1,68615
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 area4840 Å2
ΔGint-94 kcal/mol
Surface area39200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.870, 110.870, 68.210
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: 37184.148 Da / Num. of mol.: 1 / Fragment: unp residues 31-369 / Mutation: S190A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / 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: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 100 mM sodium acetate (pH 4.5), 50 mM CdCl2, 28% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 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: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.8→32.04 Å / Num. obs: 7696 / % possible obs: 99.2 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.1
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8_1069)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PV2

3pv2


Resolution: 2.8→32.038 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 32.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2754 352 4.61 %
Rwork0.2187 --
obs0.2216 7635 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→32.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2038 0 5 0 2043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082064
X-RAY DIFFRACTIONf_angle_d1.0442784
X-RAY DIFFRACTIONf_dihedral_angle_d16.431753
X-RAY DIFFRACTIONf_chiral_restr0.074346
X-RAY DIFFRACTIONf_plane_restr0.003358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.20490.32541140.28552431X-RAY DIFFRACTION100
3.2049-4.03660.28111280.21412429X-RAY DIFFRACTION100
4.0366-32.04040.26331100.20822423X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.5619-0.70781.39812.65951.5513.1699-0.0838-0.00290.8068-0.19710.0861.4713-0.4413-0.0717-0.16670.34460.0879-0.34870.38590.05210.9108-7.433324.7671-24.8569
23.92950.7615-0.01644.6273-0.61752.28620.01910.05260.42790.1376-0.03680.2555-0.0148-0.0990.00010.31930.0064-0.06960.28440.04130.42052.673418.0618-20.1145
31.5627-1.0916-1.11631.9273-0.15512.8535-0.07580.02830.4979-0.3634-0.3129-0.44420.16860.5147-0.00320.7873-0.0824-0.15320.73170.1710.523424.629536.8402-25.2635
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 8:105)
2X-RAY DIFFRACTION2(chain A and resid 106:236)
3X-RAY DIFFRACTION3(chain A and resid 237:337)

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