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- PDB-6dcj: LpoA N-terminal domain from Haemophilus influenzae; monoclinic fo... -

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Basic information

Entry
Database: PDB / ID: 6dcj
TitleLpoA N-terminal domain from Haemophilus influenzae; monoclinic form at 1.35 A resolution
ComponentsPenicillin-binding protein activator LpoA
KeywordsBIOSYNTHETIC PROTEIN / peptidoglycan synthesis / TPR-like / outer membrane lipoprotein / PROTEIN BINDING
Function / homology
Function and homology information


periplasmic side of cell outer membrane / enzyme regulator activity / peptidoglycan biosynthetic process / regulation of cell shape
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #650 / Penicillin-binding protein activator LpoA / LppC putative lipoprotein / Periplasmic binding protein-like I / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Penicillin-binding protein activator LpoA
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 Å
AuthorsVijayalakshmi, J. / 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.
History
DepositionMay 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI
Revision 1.2May 15, 2019Group: Data collection / Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Oct 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
B: Penicillin-binding protein activator LpoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5884
Polymers52,5172
Non-polymers712
Water12,304683
1
A: Penicillin-binding protein activator LpoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2942
Polymers26,2581
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Penicillin-binding protein activator LpoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2942
Polymers26,2581
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.988, 36.927, 95.359
Angle α, β, γ (deg.)90.000, 108.084, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein Penicillin-binding protein activator LpoA / PBP activator LpoA


Mass: 26258.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: lpoA, HI_1655 / Plasmid: pETBlue2
Details (production host): T7 promoter and C-terminal His6 tag
Production host: Escherichia coli (E. coli) / Strain (production host): Tuner(DE3) pLacI / References: UniProt: P45299
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 683 / 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: 2.31 Å3/Da / Density % sol: 46.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: Protein was 10 mg/ml in 0.1% beta-mercaptoethanol, 1 mM EDTA, 0.1 mM benzamidine, 20 mM Tris-HCl pH 8.0. Precipitant contained 20% polyethylene glycol 10,000, 0.1 M HEPES pH 7.5. 2 ul ...Details: Protein was 10 mg/ml in 0.1% beta-mercaptoethanol, 1 mM EDTA, 0.1 mM benzamidine, 20 mM Tris-HCl pH 8.0. Precipitant contained 20% polyethylene glycol 10,000, 0.1 M HEPES pH 7.5. 2 ul protein mixed with 2 ul precipitant on silated cover slip and equilibrated over a reservoir containing 1 ml precipitant.
PH range: 7.5-8.0

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Data collection

DiffractionMean temperature: 140 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Nov 12, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.35→34.5 Å / Num. obs: 91763 / % possible obs: 90.3 % / Redundancy: 3.28 % / Biso Wilson estimate: 15.58 Å2 / Rmerge(I) obs: 0.047 / Rrim(I) all: 0.047 / Χ2: 0.97 / Net I/σ(I): 13.1 / Num. measured all: 303668 / Scaling rejects: 2279
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsΧ2% possible all
1.35-1.42.130.2622.960121.0759.9
1.4-1.452.40.2293.775261.174.6
1.45-1.522.850.1844.691350.9990.8
1.52-1.63.520.1515.8101200.9699.4
1.6-1.73.580.1137.5100310.9199.6
1.7-1.833.620.0859.9101330.8999.9
1.83-2.023.660.06213.2100660.8899.6
2.02-2.313.580.04319.6101340.999.3
2.31-2.913.590.03824.7101651.0299.5
2.91-34.53.160.03429.884411.1880.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2 Å34.44 Å
Translation2 Å34.44 Å

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
d*TREK8.0Idata reduction
d*TREK8.0Idata scaling
PHASER2.7.2phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P29

4p29


Resolution: 1.35→34.44 Å / SU ML: 0.1352 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.9643
RfactorNum. reflection% reflection
Rfree0.1899 7328 8.02 %
Rwork0.1554 --
obs0.1582 91406 90.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 25.85 Å2
Refinement stepCycle: LAST / Resolution: 1.35→34.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3519 0 2 683 4204
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00643712
X-RAY DIFFRACTIONf_angle_d0.8675046
X-RAY DIFFRACTIONf_chiral_restr0.06570
X-RAY DIFFRACTIONf_plane_restr0.0048678
X-RAY DIFFRACTIONf_dihedral_angle_d13.3151423
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.370.29641520.26051722X-RAY DIFFRACTION56.07
1.37-1.380.28921710.23991830X-RAY DIFFRACTION60.29
1.38-1.40.28371670.22432023X-RAY DIFFRACTION65.81
1.4-1.420.2411970.21832177X-RAY DIFFRACTION70.3
1.42-1.430.26931970.212285X-RAY DIFFRACTION74.92
1.43-1.450.25712150.18582458X-RAY DIFFRACTION80.83
1.45-1.480.23032380.17152679X-RAY DIFFRACTION85.9
1.48-1.50.22722320.15882786X-RAY DIFFRACTION91.43
1.5-1.520.22312700.14933006X-RAY DIFFRACTION97.41
1.52-1.550.18992540.14753062X-RAY DIFFRACTION99.31
1.55-1.570.18482570.14333072X-RAY DIFFRACTION99.28
1.57-1.60.20282940.13773066X-RAY DIFFRACTION99.67
1.6-1.630.17762580.13893036X-RAY DIFFRACTION99.46
1.63-1.660.17192550.14213074X-RAY DIFFRACTION99.55
1.66-1.70.17212860.14063092X-RAY DIFFRACTION99.85
1.7-1.740.18362590.13973084X-RAY DIFFRACTION99.88
1.74-1.780.18882600.13293058X-RAY DIFFRACTION99.85
1.78-1.830.16852650.13883118X-RAY DIFFRACTION99.73
1.83-1.890.18252710.14343027X-RAY DIFFRACTION99.52
1.89-1.950.16572680.14453131X-RAY DIFFRACTION99.44
1.95-2.020.17462800.14023038X-RAY DIFFRACTION99.7
2.02-2.10.17312650.13773078X-RAY DIFFRACTION99.52
2.1-2.190.16142770.12983084X-RAY DIFFRACTION99.35
2.19-2.310.1712540.13173117X-RAY DIFFRACTION99.15
2.31-2.450.16612760.13663075X-RAY DIFFRACTION99.44
2.45-2.640.17892650.14163111X-RAY DIFFRACTION99.56
2.64-2.910.1792710.14563084X-RAY DIFFRACTION99.26
2.91-3.330.16482620.15693069X-RAY DIFFRACTION97.45
3.33-4.190.2082250.17942545X-RAY DIFFRACTION80.71
4.19-34.450.29121870.25872091X-RAY DIFFRACTION64.04

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