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- PDB-6pny: X-ray Structure of Flpp3 -

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Basic information

Entry
Database: PDB / ID: 6pny
TitleX-ray Structure of Flpp3
ComponentsFlpp3
KeywordsALLERGEN / Virulence Determinant / Lipoprotein
Function / homologyLipoprotein Flpp3-like / Protein of unknown function (DUF3568) / Prokaryotic membrane lipoprotein lipid attachment site profile. / Uncharacterized protein / Hypothetical lipoprotein
Function and homology information
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsZook, J.D. / Shekhar, M. / Hansen, D.T. / Conrad, C. / Grant, T.D. / Gupta, C. / White, T. / Barty, A. / Basu, S. / Zhao, Y. ...Zook, J.D. / Shekhar, M. / Hansen, D.T. / Conrad, C. / Grant, T.D. / Gupta, C. / White, T. / Barty, A. / Basu, S. / Zhao, Y. / Zatsepin, N.A. / Ishchenko, A. / Batyuk, A. / Gati, C. / Li, C. / Galli, L. / Coe, J. / Hunter, M. / Liang, M. / Weierstall, U. / Nelson, G. / James, D. / Stauch, B. / Craciunescu, F. / Thifault, D. / Liu, W. / Cherezov, V. / Singharoy, A. / Fromme, P.
CitationJournal: Structure / Year: 2020
Title: XFEL and NMR Structures of Francisella Lipoprotein Reveal Conformational Space of Drug Target against Tularemia.
Authors: Zook, J. / Shekhar, M. / Hansen, D. / Conrad, C. / Grant, T. / Gupta, C. / White, T. / Barty, A. / Basu, S. / Zhao, Y. / Zatsepin, N. / Ishchenko, A. / Batyuk, A. / Gati, C. / Li, C. / ...Authors: Zook, J. / Shekhar, M. / Hansen, D. / Conrad, C. / Grant, T. / Gupta, C. / White, T. / Barty, A. / Basu, S. / Zhao, Y. / Zatsepin, N. / Ishchenko, A. / Batyuk, A. / Gati, C. / Li, C. / Galli, L. / Coe, J. / Hunter, M. / Liang, M. / Weierstall, U. / Nelson, G. / James, D. / Stauch, B. / Craciunescu, F. / Thifault, D. / Liu, W. / Cherezov, V. / Singharoy, A. / Fromme, P.
History
DepositionJul 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 20, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
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

Downloads & links

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Assembly

Deposited unit
A: Flpp3


Theoretical massNumber of molelcules
Total (without water)13,3301
Polymers13,3301
Non-polymers00
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.000, 51.900, 68.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Flpp3


Mass: 13329.558 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4) (bacteria)
Strain: SCHU S4 / Schu 4 / Gene: BZ14_1359 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A454XXY1, UniProt: Q5NF33*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 1.91 Å3/Da / Density % sol: 35.76 %
Crystal growTemperature: 300 K / Method: batch mode
Details: Sodium Chloride, Calcium Chloride, Sodium Phosphate

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Data collection

DiffractionMean temperature: 300 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.425 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Apr 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.425 Å / Relative weight: 1
ReflectionResolution: 1.65→19 Å / Num. obs: 16570 / % possible obs: 100 % / Redundancy: 217 % / Biso Wilson estimate: 22.85 Å2 / Net I/σ(I): 7.8
Reflection shellResolution: 1.65→1.71 Å / Num. unique obs: 1143
Serial crystallography measurementCollection time total: 1 hours / Pulse duration: 35 fsec. / Pulse energy: 2.49 µJ / Pulse photon energy: 8.7 keV / XFEL pulse repetition rate: 120 Hz
Serial crystallography sample deliveryDescription: LCP Injection / Method: injection
Serial crystallography sample delivery injectionCarrier solvent: LCP / Flow rate: 0.16 µL/min / Injector diameter: 50 µm
Serial crystallography data reductionCrystal hits: 82157 / Frames failed index: 29458 / Frames indexed: 52699

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Processing

Software
NameVersionClassification
PHENIX1.14_3260model building
PHENIX1.14_3260refinement
iMOSFLMdata reduction
CrystFELdata scaling
MR-Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2MU4

2mu4


Resolution: 1.65→19 Å / SU ML: 0.286 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.6538
RfactorNum. reflection% reflection
Rfree0.2349 596 4.77 %
Rwork0.1975 --
obs0.1994 12490 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 25.79 Å2
Refinement stepCycle: LAST / Resolution: 1.65→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms910 0 0 118 1028
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032956
X-RAY DIFFRACTIONf_angle_d0.58441307
X-RAY DIFFRACTIONf_chiral_restr0.046146
X-RAY DIFFRACTIONf_plane_restr0.0034174
X-RAY DIFFRACTIONf_dihedral_angle_d2.1391782
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.820.36071470.32112894X-RAY DIFFRACTION99.93
1.82-2.080.27241480.21142926X-RAY DIFFRACTION100
2.08-2.620.22031480.18552970X-RAY DIFFRACTION100
2.62-19.030.21651530.18353104X-RAY DIFFRACTION99.97

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