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- PDB-5kcn: Crystal Structure of full-length LpoA from Haemophilus influenzae... -

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Basic information

Entry
Database: PDB / ID: 5kcn
TitleCrystal Structure of full-length LpoA from Haemophilus influenzae at 1.97 angstrom resolution
ComponentsPenicillin-binding protein activator LpoA
KeywordsBIOSYNTHETIC PROTEIN / Outer membrane lipoprotein / PBP1A / transpeptidase. peptidoglycan
Function / homologyPenicillin-binding protein activator LpoA / LppC putative lipoprotein / periplasmic side of cell outer membrane / enzyme regulator activity / peptidoglycan biosynthetic process / Periplasmic binding protein-like I / Tetratricopeptide-like helical domain superfamily / regulation of cell shape / Penicillin-binding protein activator LpoA
Function and homology information
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.965 Å
AuthorsSathiyamoorthy, K. / Saper, M.A.
Funding support United States, 2items
OrganizationGrant numberCountry
Phillip Morris United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI99984 United States
Citation
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.
#1: Journal: Proteins / Year: 2008
Title: Structure of YraM, a protein essential for growth of Haemophilus influenzae.
Authors: Vijayalakshmi, J. / Akerley, B.J. / Saper, M.A.
History
DepositionJun 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 8, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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

Downloads & links

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Assembly

Deposited unit
A: Penicillin-binding protein activator LpoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0462
Polymers60,0101
Non-polymers351
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.866, 68.427, 128.404
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 60010.074 Da / Num. of mol.: 1 / Fragment: UNP residues 33-575
Source method: isolated from a genetically manipulated source
Details: LpoA residues 33-575 / Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: lpoA, HI_1655 / Plasmid: pETBlue-2 / Details (production host): T7 promoter / Production host: Escherichia coli (E. coli) / Strain (production host): Origami(DE3)/pLacI / References: UniProt: P45299
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.4 Å3/Da / Density % sol: 48.79 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 1 microliter of concentrated protein (33 mg/ml in 150 mM NaCl, 50 mM Tris-HCl, pH 8.0) and 1 microliter precipitant [25% w/v PEG 1500, 0.1 M MMT buffer (20 mM DL-malic acid, 40 mM MES, 40 mM ...Details: 1 microliter of concentrated protein (33 mg/ml in 150 mM NaCl, 50 mM Tris-HCl, pH 8.0) and 1 microliter precipitant [25% w/v PEG 1500, 0.1 M MMT buffer (20 mM DL-malic acid, 40 mM MES, 40 mM Tris-HCl), pH 4.0] and 0.2 microliter 30% xylitol
Temp details: 277 for 2 days, then 295

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Data collection

DiffractionMean temperature: 125 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 13, 2009 / Details: Monochromator
RadiationMonochromator: 0.9786 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.965→50 Å / Num. obs: 42000 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 31.05 Å2 / Rmerge(I) obs: 0.058 / Net I/av σ(I): 29.518 / Net I/σ(I): 21.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.97-25.50.171199.6
2-2.045.90.1451100
2.04-2.086.40.131199.7
2.08-2.126.60.108199.9
2.12-2.176.60.091199.9
2.17-2.226.60.082199.9
2.22-2.276.30.11199.7
2.27-2.346.60.068199.8
2.34-2.46.60.058199.7
2.4-2.486.60.057199.9
2.48-2.576.70.054199.9
2.57-2.676.70.06199.6
2.67-2.86.70.0561100
2.8-2.946.70.0491100
2.94-3.136.70.0411100
3.13-3.376.70.0391100
3.37-3.716.70.0481100
3.71-4.246.70.053199.9
4.24-5.356.60.053199.8
5.35-506.10.076198.7

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Processing

Software
NameVersionClassification
PHENIX(dev_2376: ???)refinement
DENZO1.99.2data reduction
SCALEPACK1.99.1data scaling
PHASER2.1.4phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P29 and 3CKM

4p29

3ckm


Resolution: 1.965→31.783 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2142 2021 4.82 %
Rwork0.1774 --
obs0.1792 41907 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.965→31.783 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4184 0 1 392 4577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044281
X-RAY DIFFRACTIONf_angle_d0.6245824
X-RAY DIFFRACTIONf_dihedral_angle_d14.9452612
X-RAY DIFFRACTIONf_chiral_restr0.041661
X-RAY DIFFRACTIONf_plane_restr0.004775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9645-2.03480.24141960.20733819X-RAY DIFFRACTION97
2.0348-2.11620.24071990.19213942X-RAY DIFFRACTION100
2.1162-2.21250.2322000.18553970X-RAY DIFFRACTION100
2.2125-2.32910.24911850.21283916X-RAY DIFFRACTION99
2.3291-2.4750.2392110.18773957X-RAY DIFFRACTION100
2.475-2.6660.24332000.18633982X-RAY DIFFRACTION100
2.666-2.93410.22412050.1923978X-RAY DIFFRACTION100
2.9341-3.35830.23112120.19224020X-RAY DIFFRACTION100
3.3583-4.22950.182060.15834067X-RAY DIFFRACTION100
4.2295-31.78720.19812070.16114235X-RAY DIFFRACTION100
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)
11.4051-0.0039-0.07220.7650.03441.0262-0.25830.1793-0.4390.23380.02010.08770.4515-0.2013-0.11910.4505-0.08350.20490.3208-0.07530.471920.78485.188166.1079
20.42870.5659-0.47891.3179-0.69871.7749-0.0468-0.0401-0.0906-0.0419-0.03550.0517-0.0507-0.0178-00.2339-0.01070.00630.2277-0.00050.251427.418228.305653.5149
31.38750.1229-0.14151.7116-0.2451.1054-0.01470.08210.0254-0.3161-0.0442-0.1060.10240.0218-00.3042-0.00350.01460.21210.00860.179726.489519.541613.3537
40.85250.6488-1.46032.1022-0.52110.6923-0.1373-0.13110.1566-0.29460.28370.48730.3996-0.06430.04570.3101-0.2081-0.11260.63090.16230.5223-2.367512.052625.3819
50.55570.2305-0.64230.8162-1.08070.79820.0420.03520.1385-0.05940.15810.18730.1045-0.17410.0060.1999-0.0127-0.0350.30250.02780.274510.942825.185721.2772
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 34:119)
2X-RAY DIFFRACTION2(chain A and resid 120:250)
3X-RAY DIFFRACTION3(chain A and resid 251:359)
4X-RAY DIFFRACTION4(chain A and resid 360:502)
5X-RAY DIFFRACTION5(chain A and resid 503:573)

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