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- PDB-5vbg: Crystal Structure of full-length LpoA, Monoclinic form 1, from Ha... -

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Basic information

Entry
Database: PDB / ID: 5vbg
TitleCrystal Structure of full-length LpoA, Monoclinic form 1, from Haemophilus influenzae
ComponentsPenicillin-binding protein activator LpoA
KeywordsBIOSYNTHETIC PROTEIN / Gram-negative bacteria / Outer membrane lipoprotein / Lipoprotein activator of PBP1A / 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 / molecular replacement / Resolution: 2.8 Å
AuthorsSathiyamoorthy, K. / Saper, M.A.
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
DepositionMar 29, 2017Deposition 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 1.3Oct 4, 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
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,5973
Polymers60,5261
Non-polymers712
Water43224
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)67.458, 69.344, 73.577
Angle α, β, γ (deg.)90.000, 110.180, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 60525.926 Da / Num. of mol.: 1 / Fragment: UNP residues 33-575
Source method: isolated from a genetically manipulated source
Details: No tags present
Source: (gene. exp.) Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (bacteria)
Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: lpoA, HI_1655 / Plasmid: pETBlue-2 / Details (production host): T7 / 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.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.68 Å3/Da / Density % sol: 54.16 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: Drops were comprised of 1 microliter of concentrated protein (33 mg/ml in 150 mM NaCl, 50 mM Tris-HCl, pH 8.0), 1 microliter precipitant (8% w/v polyethylene glycol 4000, sodium acetate ...Details: Drops were comprised of 1 microliter of concentrated protein (33 mg/ml in 150 mM NaCl, 50 mM Tris-HCl, pH 8.0), 1 microliter precipitant (8% w/v polyethylene glycol 4000, sodium acetate trihydrate, pH 4.6), and 0.2 microliter 30% xylitol. The cryoprotectant was 15% glycerol in the precipitant solution. Crystals frozen in liquid nitrogen.
PH range: 6.0-7.0

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Data collection

DiffractionMean temperature: 145 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 7, 2010 / Details: monochromator
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 14455 / % possible obs: 90.1 % / Redundancy: 3.1 % / Biso Wilson estimate: 50.28 Å2 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.072 / Rrim(I) all: 0.131 / Χ2: 1.117 / Net I/σ(I): 7.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.871.80.4010.7170.3360.5261.06740.7
2.87-2.941.90.3290.8860.2610.4220.94957.1
2.94-3.022.20.3510.7810.2620.440.97772.7
3.02-3.12.50.3360.8120.2390.4151.01986.7
3.1-3.2130.2830.8970.1880.3411.01796.8
3.21-3.323.20.2380.9180.1550.2851.02799
3.32-3.453.30.1820.950.1170.2171.09799.8
3.45-3.613.40.1550.9620.0990.1841.299.8
3.61-3.83.40.1260.9690.0810.1511.07799.9
3.8-4.043.40.1070.9750.0690.1281.18299.9
4.04-4.353.30.0910.980.0590.1091.246100
4.35-4.793.40.0790.9890.050.0941.26399.7
4.79-5.483.30.080.9890.0510.0951.259100
5.48-6.93.30.0910.9860.0590.1090.97499.8
6.9-503.20.0720.9920.0470.0871.06299.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-20002.39data scaling
PHENIXdev-2376refinement
PDB_EXTRACT3.22data extraction
HKL-20002.39data reduction
PHASERphasing
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KCN

5kcn


Resolution: 2.8→35.977 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 26.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2464 1371 5.25 %Random selection
Rwork0.2047 24757 --
obs0.207 26128 84.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.38 Å2 / Biso mean: 56.4417 Å2 / Biso min: 23.16 Å2
Refinement stepCycle: final / Resolution: 2.8→35.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4221 0 2 24 4247
Biso mean--41.86 42.83 -
Num. residues----543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024324
X-RAY DIFFRACTIONf_angle_d0.4475884
X-RAY DIFFRACTIONf_chiral_restr0.036667
X-RAY DIFFRACTIONf_plane_restr0.002785
X-RAY DIFFRACTIONf_dihedral_angle_d9.2842641
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 (%)
2.8001-2.90020.3898580.31781007106535
2.9002-3.01620.358860.30951669175557
3.0162-3.15340.34961480.28432348249681
3.1534-3.31960.34031700.27312729289995
3.3196-3.52740.30691560.24072834299097
3.5274-3.79950.24361460.22082837298397
3.7995-4.18130.25931580.18632865302397
4.1813-4.78520.22651250.1592875300097
4.7852-6.02420.17581790.18412825300497
6.0242-35.98030.18021450.16782768291395
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)
11.0011-1.33790.75522.1781-0.86280.7932-0.0318-0.0492-0.04670.08320.02950.0891-0.1093-0.0386-00.3509-0.02020.01830.3496-0.0430.3549-7.370916.6234-54.152
21.83550.7682-0.5821.32390.13420.32720.07420.06470.01860.0935-0.0734-0.1675-0.00990.029500.41120.0481-0.06190.3745-0.02240.292812.78215.7254-17.005
33.1029-0.9794-0.04270.9684-0.14910.2611-0.00930.03560.02210.0704-0.1230.0484-0.0585-0.063-00.476-0.02980.03220.4557-0.04810.435-9.817417.9202-13.8201
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 245 )A33 - 245
2X-RAY DIFFRACTION2chain 'A' and (resid 246 through 376 )A246 - 376
3X-RAY DIFFRACTION3chain 'A' and (resid 377 through 575 )A377 - 575

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