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- PDB-7rqf: Crystal Structure of LbcA (lipoprotein binding partner of CtpA) o... -

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Basic information

Entry
Database: PDB / ID: 7rqf
TitleCrystal Structure of LbcA (lipoprotein binding partner of CtpA) of Pseudomonas aeruginosa
ComponentsTPR repeat-containing protein PA4667
KeywordsPROTEIN BINDING / LbcA / CtpA / lipoprotein binding / membrane
Function / homology: / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / TPR repeat-containing protein PA4667
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.5 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 1.2Nov 6, 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

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Assembly

Deposited unit
A: TPR repeat-containing protein PA4667
B: TPR repeat-containing protein PA4667


Theoretical massNumber of molelcules
Total (without water)123,3442
Polymers123,3442
Non-polymers00
Water00
1
A: TPR repeat-containing protein PA4667


Theoretical massNumber of molelcules
Total (without water)61,6721
Polymers61,6721
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TPR repeat-containing protein PA4667


Theoretical massNumber of molelcules
Total (without water)61,6721
Polymers61,6721
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.699, 120.699, 221.943
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein TPR repeat-containing protein PA4667


Mass: 61671.832 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: PA4667 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P42810
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: 3.91 Å3/Da / Density % sol: 68.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M sodium acetate, pH 4.6, and 1.9 M ammonium dihydrogen phosphate at a concentration of 45 mg/mL
PH range: 4.4-4.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 3.5→94.57 Å / Num. obs: 24325 / % possible obs: 100 % / Redundancy: 22.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.183 / Net I/σ(I): 13.2
Reflection shellResolution: 3.5→3.69 Å / Num. unique obs: 3487 / CC1/2: 0.566

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Processing

Software
NameVersionClassification
PHENIX(1.19_4092)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.5→60.39 Å / SU ML: 0.61 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2806 1198 4.93 %
Rwork0.2452 --
obs0.247 24277 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→60.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8352 0 0 0 8352
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038490
X-RAY DIFFRACTIONf_angle_d0.60811484
X-RAY DIFFRACTIONf_dihedral_angle_d3.5751172
X-RAY DIFFRACTIONf_chiral_restr0.0371248
X-RAY DIFFRACTIONf_plane_restr0.0041546
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.640.43211120.35432559X-RAY DIFFRACTION100
3.64-3.810.40461240.31112518X-RAY DIFFRACTION100
3.81-4.010.34541180.30632550X-RAY DIFFRACTION100
4.01-4.260.36651300.29962515X-RAY DIFFRACTION100
4.26-4.590.37431210.27672539X-RAY DIFFRACTION100
4.59-5.050.28181120.25082593X-RAY DIFFRACTION100
5.05-5.780.33911610.2812523X-RAY DIFFRACTION100
5.78-7.270.30421750.24872566X-RAY DIFFRACTION100
7.28-60.390.181450.17942716X-RAY DIFFRACTION100

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