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- PDB-6dr3: Crystal structure of E. coli LpoA amino terminal domain -

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Basic information

Entry
Database: PDB / ID: 6dr3
TitleCrystal structure of E. coli LpoA amino terminal domain
ComponentsPenicillin-binding protein activator LpoA
KeywordsBIOSYNTHETIC PROTEIN / TPR-like motifs OUTER MEMBRANE LIPOPROTEIN ACTIVATOR OF PBP1A PEPTIDOGLYCAN
Function / homology
Function and homology information


periplasmic side of cell outer membrane / peptidoglycan biosynthetic process / hydrolase activity, hydrolyzing O-glycosyl compounds / enzyme regulator activity / cell outer membrane / regulation of cell shape / periplasmic space / enzyme binding
Similarity search - Function
Penicillin-binding protein activator LpoA / LppC putative lipoprotein / Lytic transglycosylase, superhelical U-shaped / Periplasmic binding protein-like I / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Penicillin-binding protein activator LpoA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.101 Å
AuthorsKelley, A.C. / Saper, M.A.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Crystal structures of the amino-terminal domain of LpoA from Escherichia coli and Haemophilus influenzae.
Authors: Kelley, A. / Vijayalakshmi, J. / Saper, M.A.
#1: Journal: J. Biol. Chem. / Year: 2017
Title: Structural analyses of the Haemophilus influenzae peptidoglycan synthase activator LpoA suggest multiple conformations in solution.
Authors: Sathiyamoorthy, K. / Vijayalakshmi, J. / Tirupati, B. / Fan, L. / Saper, M.A.
#2: Journal: Structure / Year: 2014
Title: Elongated structure of the outer-membrane activator of peptidoglycan synthesis LpoA: implications for PBP1A stimulation.
Authors: Jean, N.L. / Bougault, C.M. / Lodge, A. / Derouaux, A. / Callens, G. / Egan, A.J. / Ayala, I. / Lewis, R.J. / Vollmer, W. / Simorre, J.P.
History
DepositionJun 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Penicillin-binding protein activator LpoA


Theoretical massNumber of molelcules
Total (without water)25,1781
Polymers25,1781
Non-polymers00
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.001, 70.001, 97.802
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Penicillin-binding protein activator LpoA / PBP activator LpoA / Lipoprotein activator of PBP from the outer membrane A


Mass: 25178.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: lpoA, yraM, b3147, JW3116 / Plasmid: pMCSG7-EcLpoA-N(31-252)
Details (production host): Expresses of fusion of His6, TeV cleavage sequence, and EcLpoA-N(31-252)
Cell line (production host): Origami 2(DE3) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): Origami 2(DE3) / Variant (production host): Origami 2(DE3) / References: UniProt: P45464
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O

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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: 2.38 Å3/Da / Density % sol: 48.3 % / Description: needles with square cross-section
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Drops contained 0.5 ul protein and 0.5 ul precipitant and equilibrated against precipitant by vapor diffusion. Protein: 19 mg/ml in 50 mM NaCl, 1 mM dithiothreitol, 50 mM TrisHCl pH 7.5. ...Details: Drops contained 0.5 ul protein and 0.5 ul precipitant and equilibrated against precipitant by vapor diffusion. Protein: 19 mg/ml in 50 mM NaCl, 1 mM dithiothreitol, 50 mM TrisHCl pH 7.5. Precipitant contained: 0.03 M magnesium chloride hexahydrate, 0.03 M calcium chloride dihydrate, 5% glycerol, 0.1 M Buffer System 1, pH 6.5, 10% PEG 20,000, 17% PEG 550 MME Buffer System 1: 30 mL MES (pH 3.11) was titrated with 24.1 mL Imidazole (pH 10.23) to a final pH of 6.5

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Data collection

DiffractionMean temperature: 140 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97717 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 2, 2017 / Details: mirrors
RadiationMonochromator: Kohzu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97717 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 14791 / % possible obs: 99.8 % / Redundancy: 10.9 % / Biso Wilson estimate: 27.23 Å2 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.032 / Rrim(I) all: 0.109 / Χ2: 0.959 / Net I/σ(I): 6.7 / Num. measured all: 160798
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.185.70.7614510.6920.3390.8370.91999.6
2.18-2.267.60.56314360.880.2160.6051.039100
2.26-2.378.40.42814400.9310.1570.4570.962100
2.37-2.4910.80.33814540.9690.1070.3550.941100
2.49-2.6511.50.26714420.9810.0820.2790.942100
2.65-2.8513.20.19814760.9920.0560.2060.962100
2.85-3.14140.13614750.9960.0370.1410.976100
3.14-3.5912.60.08314780.9980.0240.0870.997100
3.59-4.5212.90.05515230.9990.0160.0570.985100
4.52-3011.50.04416160.9990.0130.0460.86799

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.91 Å22.7 Å
Translation5.91 Å22.7 Å

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Processing

Software
NameVersionClassification
DENZO2.3.10data reduction
HKL-20002.3.10data scaling
PHASER2.7.2phasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P29

4p29


Resolution: 2.101→22.697 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.47 / Phase error: 20.19
RfactorNum. reflection% reflection
Rfree0.2132 1465 9.99 %
Rwork0.1771 --
obs0.1808 14660 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 158.63 Å2 / Biso mean: 42.4992 Å2 / Biso min: 14.45 Å2
Refinement stepCycle: final / Resolution: 2.101→22.697 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1769 0 0 151 1920
Biso mean---40.02 -
Num. residues----223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021806
X-RAY DIFFRACTIONf_angle_d0.4412449
X-RAY DIFFRACTIONf_chiral_restr0.033270
X-RAY DIFFRACTIONf_plane_restr0.001327
X-RAY DIFFRACTIONf_dihedral_angle_d11.0441116
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1007-2.17570.28121350.24911223135894
2.1757-2.26280.25111440.21812931437100
2.2628-2.36570.26431430.21312961439100
2.3657-2.49020.23941440.204113021446100
2.4902-2.6460.22981440.188812971441100
2.646-2.850.22651480.185213251473100
2.85-3.13610.2071470.189713181465100
3.1361-3.58840.22091480.156913331481100
3.5884-4.51520.17791530.135613621515100
4.5152-22.6980.19011590.177814461605100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.1807-1.11730.22714.29281.25944.38170.01680.24760.1072-0.135-0.118-0.198-0.08590.17770.07950.1362-0.0138-0.01250.15630.05680.1552.3786-25.3257-20.136
22.06122.288-1.13375.3034-2.6742.99760.07420.03730.05620.1282-0.01980.0709-0.0408-0.1544-0.05270.1428-0.0235-0.00080.2136-0.00210.1794-13.3947-41.70510.3184
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 111 )A30 - 111
2X-RAY DIFFRACTION2chain 'A' and (resid 112 through 249 )A112 - 249

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