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- PDB-3sti: Crystal structure of the protease domain of DegQ from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 3sti
TitleCrystal structure of the protease domain of DegQ from Escherichia coli
ComponentsProtease degQ
KeywordsHYDROLASE / serine protease / PDZ domain / protease / chaperone
Function / homology
Function and homology information


peptidase Do / protein quality control for misfolded or incompletely synthesized proteins / proteolysis involved in protein catabolic process / peptidase activity / periplasmic space / serine-type endopeptidase activity / proteolysis / identical protein binding
Similarity search - Function
Peptidase S1C, Do / Peptidase S1C / Trypsin-like peptidase domain / PDZ 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 ...Peptidase S1C, Do / Peptidase S1C / Trypsin-like peptidase domain / PDZ 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 / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Periplasmic pH-dependent serine endoprotease DegQ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSawa, J. / Malet, H. / Krojer, T. / Canellas, F. / Ehrmann, M. / Clausen, T.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Molecular adaptation of the DegQ protease to exert protein quality control in the bacterial cell envelope.
Authors: Sawa, J. / Malet, H. / Krojer, T. / Canellas, F. / Ehrmann, M. / Clausen, T.
History
DepositionJul 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protease degQ
B: Protease degQ
C: Protease degQ


Theoretical massNumber of molelcules
Total (without water)76,9703
Polymers76,9703
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-26 kcal/mol
Surface area23270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.868, 70.868, 152.013
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Protease degQ


Mass: 25656.779 Da / Num. of mol.: 3 / Fragment: UNP residues 28-264
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: degQ, hhoA, b3234, JW3203 / Production host: Escherichia coli (E. coli)
References: UniProt: P39099, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases

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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: 2.85 Å3/Da / Density % sol: 56.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7
Details: 1.6M Ammonium sulfate, 3% PEG 400, 0.1M Hepes, pH7.0 , VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 7, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 23603 / Num. obs: 23603 / % possible obs: 96.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 60.74 Å2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
BUSTER2.8.0refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→19.8 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.86 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1204 5.1 %RANDOM
Rwork0.222 ---
obs0.223 23603 --
all-23603 --
Displacement parametersBiso mean: 51.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.6127 Å20 Å20 Å2
2---0.6127 Å20 Å2
3---1.2255 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4016 0 0 0 4016
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014057HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.255487HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1890SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes118HARMONIC2
X-RAY DIFFRACTIONt_gen_planes581HARMONIC5
X-RAY DIFFRACTIONt_it4057HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.97
X-RAY DIFFRACTIONt_other_torsion3.22
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion568SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4390SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.71 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.3044 144 4.69 %
Rwork0.2548 2929 -
all0.2571 3073 -

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