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- PDB-7rqh: Crystal Structure of carboxyl-terminal processing protease A muta... -

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Basic information

Entry
Database: PDB / ID: 7rqh
TitleCrystal Structure of carboxyl-terminal processing protease A mutant S302A, CtpA_S302A, of Pseudomonas aeruginosa
ComponentsProbable carboxyl-terminal protease
KeywordsHYDROLASE / CtpA / CTP
Function / homology
Function and homology information


cell envelope organization / cell wall biogenesis / protein secretion by the type III secretion system / cell envelope / outer membrane-bounded periplasmic space / endopeptidase activity / periplasmic space / serine-type endopeptidase activity / signal transduction / proteolysis / plasma membrane
Similarity search - Function
: / Activating protease CtpB N-terminal domain / C-terminal-processing peptidase S41A / tail specific protease / Tail specific protease / Peptidase family S41 / PDZ domain 6 / PDZ domain / ClpP/crotonase-like domain superfamily / PDZ domain profile. ...: / Activating protease CtpB N-terminal domain / C-terminal-processing peptidase S41A / tail specific protease / Tail specific protease / Peptidase family S41 / PDZ domain 6 / PDZ domain / ClpP/crotonase-like domain superfamily / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
Probable carboxyl-terminal protease
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsHsu, H.C. / Li, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 AI136901 United States
CitationJournal: Mbio / Year: 2022
Title: Pseudomonas aeruginosa C-Terminal Processing Protease CtpA Assembles into a Hexameric Structure That Requires Activation by a Spiral-Shaped Lipoprotein-Binding Partner.
Authors: Hsu, H.C. / Wang, M. / Kovach, A. / Darwin, A.J. / Li, H.
History
DepositionAug 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable carboxyl-terminal protease
B: Probable carboxyl-terminal protease


Theoretical massNumber of molelcules
Total (without water)85,6132
Polymers85,6132
Non-polymers00
Water00
1
A: Probable carboxyl-terminal protease

A: Probable carboxyl-terminal protease

A: Probable carboxyl-terminal protease

B: Probable carboxyl-terminal protease

B: Probable carboxyl-terminal protease

B: Probable carboxyl-terminal protease


Theoretical massNumber of molelcules
Total (without water)256,8386
Polymers256,8386
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
crystal symmetry operation4_455x-1/3,y+1/3,z+1/31
crystal symmetry operation5_455-y-1/3,x-y+1/3,z+1/31
crystal symmetry operation6_455-x+y-1/3,-x+1/3,z+1/31
Buried area18670 Å2
ΔGint-152 kcal/mol
Surface area70410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.650, 189.650, 131.105
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 Probable carboxyl-terminal protease


Mass: 42806.336 Da / Num. of mol.: 2 / Mutation: S302A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: PA5134 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9HU50

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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: 5.3 Å3/Da / Density % sol: 76.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.1 M sodium acetate, pH 4.0, and 0.6 M ammonium dihydrogen phosphate at a concentration of 33 mg/mL
PH range: 4.0 -4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07803 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07803 Å / Relative weight: 1
ReflectionResolution: 3.2→94.82 Å / Num. obs: 28884 / % possible obs: 99.6 % / Redundancy: 10.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Net I/σ(I): 15.6
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 10.6 % / Num. unique obs: 4245 / CC1/2: 0.524 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.19_4092)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7RPQ

7rpq


Resolution: 3.2→43.03 Å / SU ML: 0.61 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 32.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2654 1415 4.9 %
Rwork0.2409 --
obs0.2422 28849 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→43.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3931 0 0 0 3931
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033977
X-RAY DIFFRACTIONf_angle_d0.7395383
X-RAY DIFFRACTIONf_dihedral_angle_d4.155555
X-RAY DIFFRACTIONf_chiral_restr0.045641
X-RAY DIFFRACTIONf_plane_restr0.005703
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.310.47641510.37892723X-RAY DIFFRACTION100
3.31-3.450.33851630.33632768X-RAY DIFFRACTION100
3.45-3.60.30081210.29222771X-RAY DIFFRACTION99
3.6-3.790.28571410.25922744X-RAY DIFFRACTION100
3.79-4.030.32121370.27892705X-RAY DIFFRACTION98
4.03-4.340.21511360.21552730X-RAY DIFFRACTION99
4.34-4.780.24551250.21022768X-RAY DIFFRACTION100
4.78-5.470.24161420.22392775X-RAY DIFFRACTION100
5.47-6.890.29891380.25182762X-RAY DIFFRACTION100
6.89-43.030.2411610.22342688X-RAY DIFFRACTION98

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