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- PDB-7rpq: Crystal Structure of carboxyl-terminal processing protease A, Ctp... -

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Basic information

Entry
Database: PDB / ID: 7rpq
TitleCrystal Structure of carboxyl-terminal processing protease A, CtpA, 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 / SAD / Resolution: 3.3 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 4, 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 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)86,3422
Polymers86,3422
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)259,0256
Polymers259,0256
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 area19550 Å2
ΔGint-149 kcal/mol
Surface area69800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.489, 187.489, 132.011
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

#1: Protein Probable carboxyl-terminal protease


Mass: 43170.910 Da / Num. of mol.: 2
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
Has ligand of interestN
Has protein modificationY

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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: 5.2 Å3/Da / Density % sol: 76.35 %
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: 31-ID / Wavelength: 0.97931 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 3.3→93.75 Å / Num. obs: 26048 / % possible obs: 100 % / Redundancy: 11.6 % / Biso Wilson estimate: 90.56 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.167 / Net I/σ(I): 10.8
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.912 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3847 / CC1/2: 0.434 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.19_4092)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.3→39.83 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 28.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2636 1219 4.68 %
Rwork0.2363 --
obs0.2375 26026 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→39.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3933 0 0 0 3933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033979
X-RAY DIFFRACTIONf_angle_d0.7575385
X-RAY DIFFRACTIONf_dihedral_angle_d4.202555
X-RAY DIFFRACTIONf_chiral_restr0.046641
X-RAY DIFFRACTIONf_plane_restr0.005703
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.430.34481630.33412737X-RAY DIFFRACTION100
3.43-3.590.33731100.30772790X-RAY DIFFRACTION100
3.59-3.780.26771480.26812764X-RAY DIFFRACTION100
3.78-4.010.26951350.25282746X-RAY DIFFRACTION100
4.01-4.320.2691420.21532755X-RAY DIFFRACTION100
4.32-4.760.23011480.19542713X-RAY DIFFRACTION100
4.76-5.440.24241310.21022768X-RAY DIFFRACTION100
5.45-6.850.27871430.24742755X-RAY DIFFRACTION100
6.85-39.830.2343990.22072779X-RAY DIFFRACTION100

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