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- PDB-7fds: High resolution crystal structure of LpqH from Mycobacterium tube... -

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Basic information

Entry
Database: PDB / ID: 7fds
TitleHigh resolution crystal structure of LpqH from Mycobacterium tuberculosis
ComponentsLipoprotein LpqH
KeywordsLIPID BINDING PROTEIN
Function / homology
Function and homology information


symbiont-mediated perturbation of host immune response / bacterial extracellular vesicle / biological process involved in interaction with host / peptidoglycan-based cell wall / host cell cytoplasm / defense response to bacterium / host cell surface receptor binding / cell surface / plasma membrane
Similarity search - Function
19kDa lipoprotein antigen / Mycobacterium 19 kDa lipoprotein antigen / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.258 Å
AuthorsKundapura, S.V. / Chatterjee, S. / Samanta, D. / Ramagopal, U.A.
CitationJournal: Int.J.Biol.Macromol. / Year: 2022
Title: High-resolution crystal structure of LpqH, an immunomodulatory surface lipoprotein of Mycobacterium tuberculosis reveals a distinct fold and a conserved cleft on its surface.
Authors: Chatterjee, S. / Kundapura, S.V. / Basak, A.J. / Mukherjee, D. / Dash, S. / Ganguli, N. / Das, A.K. / Mukherjee, G. / Samanta, D. / Ramagopal, U.A.
History
DepositionJul 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Database references / Derived calculations / Category: atom_type / citation / citation_author
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipoprotein LpqH
B: Lipoprotein LpqH


Theoretical massNumber of molelcules
Total (without water)25,5842
Polymers25,5842
Non-polymers00
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-14 kcal/mol
Surface area10500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.900, 78.510, 42.180
Angle α, β, γ (deg.)90.000, 107.340, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lipoprotein LpqH / 19 kDa lipoprotein antigen / Putative transporter LpqH / p19


Mass: 12792.177 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: lpqH / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: P9WK61
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.85 Å3/Da / Density % sol: 33.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.3 / Details: 0.2M Ammonium sulphate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.258→28.557 Å / Num. obs: 49917 / % possible obs: 99.1 % / Redundancy: 4.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.047 / Rrim(I) all: 0.078 / Rsym value: 0.067 / Net I/σ(I): 10.1
Reflection shellResolution: 1.258→1.28 Å / Rmerge(I) obs: 0.502 / Num. unique obs: 2627 / CC1/2: 0.811 / Rpim(I) all: 0.407 / Rrim(I) all: 0.649 / Rsym value: 0.58 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZJM

4zjm


Resolution: 1.258→28.557 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.031 / SU ML: 0.038 / Cross valid method: FREE R-VALUE / ESU R: 0.043 / ESU R Free: 0.044
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1779 2464 4.939 %
Rwork0.1429 47424 -
all0.145 --
obs-49888 99.106 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.54 Å2
Baniso -1Baniso -2Baniso -3
1-2.045 Å20 Å20.358 Å2
2---1.291 Å20 Å2
3----0.818 Å2
Refinement stepCycle: LAST / Resolution: 1.258→28.557 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1527 0 0 116 1643
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0131662
X-RAY DIFFRACTIONr_bond_other_d0.0060.0171563
X-RAY DIFFRACTIONr_angle_refined_deg2.4021.6382294
X-RAY DIFFRACTIONr_angle_other_deg1.7061.5743624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7425262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg51.0727.95544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.05215237
X-RAY DIFFRACTIONr_chiral_restr0.1170.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022003
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02313
X-RAY DIFFRACTIONr_nbd_refined0.1930.2256
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.21281
X-RAY DIFFRACTIONr_nbtor_refined0.1650.2792
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0930.2852
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.262
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2270.214
X-RAY DIFFRACTIONr_nbd_other0.2180.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1870.29
X-RAY DIFFRACTIONr_mcbond_it3.5161.862977
X-RAY DIFFRACTIONr_mcbond_other3.5141.86976
X-RAY DIFFRACTIONr_mcangle_it4.4332.7931228
X-RAY DIFFRACTIONr_mcangle_other4.4332.7961229
X-RAY DIFFRACTIONr_scbond_it4.7272.266685
X-RAY DIFFRACTIONr_scbond_other4.7232.267686
X-RAY DIFFRACTIONr_scangle_it5.8243.2261054
X-RAY DIFFRACTIONr_scangle_other5.8213.2281055
X-RAY DIFFRACTIONr_lrange_it5.52924.2831623
X-RAY DIFFRACTIONr_lrange_other5.51524.1921611
X-RAY DIFFRACTIONr_rigid_bond_restr12.01633225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.258-1.2910.2731930.2453477X-RAY DIFFRACTION98.0235
1.291-1.3260.2451950.2083350X-RAY DIFFRACTION98.527
1.326-1.3640.2141680.1863335X-RAY DIFFRACTION99.4323
1.364-1.4060.2291620.1683209X-RAY DIFFRACTION98.4521
1.406-1.4520.1951810.1613113X-RAY DIFFRACTION99.7275
1.452-1.5030.1951290.1353063X-RAY DIFFRACTION99.192
1.503-1.560.1661630.1192900X-RAY DIFFRACTION99.6422
1.56-1.6240.1811330.1192767X-RAY DIFFRACTION97.4135
1.624-1.6960.161090.1192713X-RAY DIFFRACTION99.3662
1.696-1.7780.2011370.132593X-RAY DIFFRACTION99.4173
1.778-1.8740.1771450.122446X-RAY DIFFRACTION99.769
1.874-1.9880.153910.1052335X-RAY DIFFRACTION98.4178
1.988-2.1240.149910.1122206X-RAY DIFFRACTION99.6962
2.124-2.2940.1441060.1122045X-RAY DIFFRACTION99.6295
2.294-2.5120.1481100.131873X-RAY DIFFRACTION100
2.512-2.8070.18880.1511703X-RAY DIFFRACTION99.4448
2.807-3.2390.199950.1541483X-RAY DIFFRACTION99.8734
3.239-3.9610.175770.1421267X-RAY DIFFRACTION99.8514
3.961-5.5740.149480.154988X-RAY DIFFRACTION98.6667
5.574-28.5570.207430.233558X-RAY DIFFRACTION99.1749

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