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- PDB-4qa8: Crystal structure of LprF from Mycobacterium bovis -

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Basic information

Entry
Database: PDB / ID: 4qa8
TitleCrystal structure of LprF from Mycobacterium bovis
ComponentsPutative lipoprotein LprF
KeywordsLIPID TRANSPORT / lipid transfer / diacylated glycolipid
Function / homology
Function and homology information


lipid transport / lipid binding / plasma membrane
Similarity search - Function
outer membrane lipoprotein receptor (LolB), chain A - #20 / LppX/LprAFG lipoprotein family / LppX_LprAFG lipoprotein / outer membrane lipoprotein receptor (LolB), chain A / Lipoprotein localisation LolA/LolB/LppX / Clam / Mainly Beta
Similarity search - Domain/homology
Chem-PJZ / Putative diacylated glycolipid transporter LprF
Similarity search - Component
Biological speciesMycobacterium bovis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsHa, N.C. / Jiao, L. / Kim, J.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Crystal structure and functional implications of LprF from Mycobacterium tuberculosis and M. bovis
Authors: Kim, J.S. / Jiao, L. / Oh, J.I. / Ha, N.C. / Kim, Y.H.
History
DepositionMay 2, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative lipoprotein LprF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2002
Polymers23,7281
Non-polymers4731
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.514, 32.381, 51.717
Angle α, β, γ (deg.)76.40, 80.79, 71.23
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Putative lipoprotein LprF


Mass: 23727.754 Da / Num. of mol.: 1 / Fragment: UNP residues 40-261
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium bovis (bacteria) / Strain: ATCC BAA-935 / AF2122/97 / Gene: lprF, Mb1403 / Production host: Escherichia coli (E. coli) / References: UniProt: P65315
#2: Chemical ChemComp-PJZ / (2R)-2-(dodecanoyloxy)propyl (4E,6E,8E,10E,12E)-pentadeca-4,6,8,10,12-pentaenoate


Mass: 472.700 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H48O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.04 Å3/Da / Density % sol: 39.65 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.1M Tris-HCl (pH 7.8), 0.2M Magnesium chloride, 28% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 23, 2012
RadiationMonochromator: double mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.1→20 Å / Num. all: 68866 / Num. obs: 68768 / % possible obs: 90.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.1-1.12182
1.12-1.14183
1.14-1.16184.6
1.16-1.18185.5
1.18-1.21186.3
1.21-1.24187.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→18.563 Å / SU ML: 0.08 / σ(F): 2.25 / Phase error: 16.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1885 3455 5.02 %RANDOM
Rwork0.1639 ---
obs0.1651 61537 90.37 %-
all-76096 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.1→18.563 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1535 0 34 156 1725
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061682
X-RAY DIFFRACTIONf_angle_d1.1592306
X-RAY DIFFRACTIONf_dihedral_angle_d15.337648
X-RAY DIFFRACTIONf_chiral_restr0.046273
X-RAY DIFFRACTIONf_plane_restr0.006306
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.1-1.11510.18541100.183234081
1.1151-1.1310.19041060.1665243083
1.131-1.14790.16791610.1516241385
1.1479-1.16580.13491290.1488245784
1.1658-1.18490.18321120.1448247186
1.1849-1.20530.16941330.1452252786
1.2053-1.22730.15371350.1378246887
1.2273-1.25090.18231210.1431254288
1.2509-1.27640.16651220.15255788
1.2764-1.30410.17741400.1407259590
1.3041-1.33450.17371270.1437258389
1.3345-1.36780.16181460.1401264391
1.3678-1.40480.16631410.1442260091
1.4048-1.44610.15591400.1431265692
1.4461-1.49280.1871460.151266692
1.4928-1.54610.16251490.1425268692
1.5461-1.6080.1761470.1578270794
1.608-1.68110.18471540.1634271694
1.6811-1.76970.20251490.1711271495
1.7697-1.88050.17231330.1717273294
1.8805-2.02550.16861430.1677276295
2.0255-2.2290.18491370.1722277396
2.229-2.55080.20071580.176280797
2.5508-3.21110.21851580.1843281997
3.2111-18.56550.20061580.1592264992

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