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- PDB-6w5q: Structure of the globular C-terminal domain of P. aeruginosa LpoP -

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Basic information

Entry
Database: PDB / ID: 6w5q
TitleStructure of the globular C-terminal domain of P. aeruginosa LpoP
ComponentsPeptidoglycan synthase activator LpoP
KeywordsPROTEIN BINDING / Lipoprotein / Activator / Cell Wall
Function / homology: / TPR repeat region circular profile. / Tetratricopeptide-like helical domain superfamily / TRIETHYLENE GLYCOL / TPR_REGION domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCaveney, N.A. / Robb, C.S. / Simorre, J.P. / Strynadka, N.C.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Structure / Year: 2020
Title: Structure of the Peptidoglycan Synthase Activator LpoP in Pseudomonas aeruginosa.
Authors: Caveney, N.A. / Egan, A.J.F. / Ayala, I. / Laguri, C. / Robb, C.S. / Breukink, E. / Vollmer, W. / Strynadka, N.C.J. / Simorre, J.P.
History
DepositionMar 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidoglycan synthase activator LpoP
B: Peptidoglycan synthase activator LpoP
C: Peptidoglycan synthase activator LpoP
D: Peptidoglycan synthase activator LpoP
E: Peptidoglycan synthase activator LpoP
F: Peptidoglycan synthase activator LpoP
G: Peptidoglycan synthase activator LpoP
H: Peptidoglycan synthase activator LpoP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,46722
Polymers97,0688
Non-polymers1,39914
Water2,594144
1
A: Peptidoglycan synthase activator LpoP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3263
Polymers12,1341
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidoglycan synthase activator LpoP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3263
Polymers12,1341
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Peptidoglycan synthase activator LpoP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3263
Polymers12,1341
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Peptidoglycan synthase activator LpoP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2302
Polymers12,1341
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Peptidoglycan synthase activator LpoP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2842
Polymers12,1341
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Peptidoglycan synthase activator LpoP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3263
Polymers12,1341
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Peptidoglycan synthase activator LpoP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2302
Polymers12,1341
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Peptidoglycan synthase activator LpoP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4224
Polymers12,1341
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.757, 154.584, 54.083
Angle α, β, γ (deg.)90.000, 90.150, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Peptidoglycan synthase activator LpoP / TPR_REGION domain-containing protein


Mass: 12133.508 Da / Num. of mol.: 8 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa / Gene: PA4699 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HV97
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.1 Å3/Da / Density % sol: 41.42 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: (30 mg/mL purified protein in 20 mM HEPES, pH 8.0, 150 mM NaCl) and 1 uL of mother liquor (0.1 M HEPES pH 7.5, 2.5 M ammonium sulfate, 1% PEG 400, 2.5% 1,2-butanediol)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→48.76 Å / Num. obs: 39974 / % possible obs: 98.7 % / Redundancy: 3.2 % / Biso Wilson estimate: 33.68 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.037 / Rrim(I) all: 0.069 / Net I/σ(I): 12.7 / Num. measured all: 129787 / Scaling rejects: 68
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.273.20.3781106234540.8640.2470.4533.298.6
9.07-48.763.10.02517745670.9990.0160.0328.695.4

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: homology model based on 5XW7

5xw7


Resolution: 2.2→48.757 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.79
RfactorNum. reflection% reflection
Rfree0.2298 1414 3.55 %
Rwork0.1942 --
obs0.1955 39858 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 110.87 Å2 / Biso mean: 41.759 Å2 / Biso min: 20.52 Å2
Refinement stepCycle: final / Resolution: 2.2→48.757 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6194 0 85 144 6423
Biso mean--60.57 42.26 -
Num. residues----834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016340
X-RAY DIFFRACTIONf_angle_d0.9878557
X-RAY DIFFRACTIONf_chiral_restr0.047933
X-RAY DIFFRACTIONf_plane_restr0.0111168
X-RAY DIFFRACTIONf_dihedral_angle_d22.6972402
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.27860.29541420.2692381998
2.2786-2.36990.26271410.2332386799
2.3699-2.47770.25631420.2306382999
2.4777-2.60830.30021410.2446384798
2.6083-2.77180.24341400.2309381198
2.7718-2.98570.25781420.2096386599
2.9857-3.28610.23511470.2016387999
3.2861-3.76150.23621460.1812383098
3.7615-4.73850.18151350.1556382798
4.7385-48.7570.2061380.176387097

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