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- PDB-4zjm: Crystal Structure of Mycobacterium tuberculosis LpqH (Rv3763) -

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Basic information

Entry
Database: PDB / ID: 4zjm
TitleCrystal Structure of Mycobacterium tuberculosis LpqH (Rv3763)
Components(Lipoprotein LpqH) x 7
KeywordsUNKNOWN FUNCTION / lipoprotein / virulence / structural genomics / PSI-2 / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.851 Å
AuthorsArbing, M.A. / Chan, S. / Kuo, E. / Harris, L.R. / Zhou, T.T. / Eisenberg, D. / TB Structural Genomics Consortium (TBSGC)
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)23616-002-06 F3:02 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)TBSGC R01 (A1068135) United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)TBSGC P01 (AI095208) United States
CitationJournal: To Be Published
Title: Crystal Structure of Mycobacterium tuberculosis LpqH (Rv3763)
Authors: Arbing, M.A. / Chan, S. / Kuo, E. / Harris, L.R. / Zhou, T.T. / Eisenberg, D.
History
DepositionApr 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 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: Lipoprotein LpqH
B: Lipoprotein LpqH
C: Lipoprotein LpqH
D: Lipoprotein LpqH
E: Lipoprotein LpqH
F: Lipoprotein LpqH
G: Lipoprotein LpqH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,28728
Polymers83,3427
Non-polymers1,94521
Water32418
1
A: Lipoprotein LpqH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3335
Polymers11,9561
Non-polymers3764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lipoprotein LpqH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4757
Polymers11,9021
Non-polymers5726
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lipoprotein LpqH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0673
Polymers11,8751
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lipoprotein LpqH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0073
Polymers11,8751
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Lipoprotein LpqH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0943
Polymers11,9021
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Lipoprotein LpqH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0943
Polymers11,9021
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Lipoprotein LpqH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2174
Polymers11,9291
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.370, 100.370, 239.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 7 types, 7 molecules ABCDEFG

#1: Protein Lipoprotein LpqH / 19 kDa lipoprotein antigen


Mass: 11956.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: lpqH, Rv3763, MTV025.111 / Plasmid: pMAPLe3 / Details (production host): pET28 derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): (DE3) / References: UniProt: P9WK61
#2: Protein Lipoprotein LpqH / 19 kDa lipoprotein antigen


Mass: 11902.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: lpqH, Rv3763, MTV025.111 / Plasmid: pMAPLe3 / Details (production host): pET28 derivative / Production host: Escherichia coli / Strain (production host): BL21 / Variant (production host): (DE3) / References: UniProt: P9WK61
#3: Protein Lipoprotein LpqH / 19 kDa lipoprotein antigen


Mass: 11875.097 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: lpqH, Rv3763, MTV025.111 / Plasmid: pMAPLe3 / Details (production host): pET28 derivative / Production host: Escherichia coli / Strain (production host): BL21 / Variant (production host): (DE3) / References: UniProt: P9WK61
#4: Protein Lipoprotein LpqH / 19 kDa lipoprotein antigen


Mass: 11875.097 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: lpqH, Rv3763, MTV025.111 / Plasmid: pMAPLe3 / Details (production host): pET28 derivative / Production host: Escherichia coli / Strain (production host): BL21 / Variant (production host): (DE3) / References: UniProt: P9WK61
#5: Protein Lipoprotein LpqH / 19 kDa lipoprotein antigen


Mass: 11902.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: lpqH, Rv3763, MTV025.111 / Plasmid: pMAPLe3 / Details (production host): pET28 derivative / Production host: Escherichia coli / Strain (production host): BL21 / Variant (production host): (DE3) / References: UniProt: P9WK61
#6: Protein Lipoprotein LpqH / 19 kDa lipoprotein antigen


Mass: 11902.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: lpqH, Rv3763, MTV025.111 / Plasmid: pMAPLe3 / Details (production host): pET28 derivative / Production host: Escherichia coli / Strain (production host): BL21 / Variant (production host): (DE3) / References: UniProt: P9WK61
#7: Protein Lipoprotein LpqH / 19 kDa lipoprotein antigen


Mass: 11929.189 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: lpqH, Rv3763, MTV025.111 / Plasmid: pMAPLe3 / Details (production host): pET28 derivative / Production host: Escherichia coli / Strain (production host): BL21 / Variant (production host): (DE3) / References: UniProt: P9WK61

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Non-polymers , 4 types, 39 molecules

#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#10: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.63 Å3/Da / Density % sol: 66.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2:1 ratio of protein to reservoir solution (2 M ammonium sulfate). 200 nanoliter drop size. Protein buffer: 50 mM HEPES, pH 7.8, 150 mM NaCl.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.85→19.832 Å / Num. obs: 29240 / % possible obs: 99.87 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 69.23 Å2 / Rmerge(I) obs: 0.1181 / Net I/σ(I): 15.22
Reflection shellResolution: 2.85→2.93 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.494 / Mean I/σ(I) obs: 1.88 / % possible all: 98.96

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
MR-Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XIN

4xin


Resolution: 2.851→19.832 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2462 2920 10.01 %Random
Rwork0.202 ---
obs0.2064 29178 99.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 86.4885 Å2
Refinement stepCycle: LAST / Resolution: 2.851→19.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5374 0 104 18 5496
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085523
X-RAY DIFFRACTIONf_angle_d1.1277528
X-RAY DIFFRACTIONf_dihedral_angle_d11.1041879
X-RAY DIFFRACTIONf_chiral_restr0.046915
X-RAY DIFFRACTIONf_plane_restr0.006975
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.851-2.89770.39731320.3591187X-RAY DIFFRACTION97
2.8977-2.94750.41681370.34371227X-RAY DIFFRACTION99
2.9475-3.00090.43661330.31991197X-RAY DIFFRACTION99
3.0009-3.05840.33351380.31491242X-RAY DIFFRACTION100
3.0584-3.12060.381370.30181227X-RAY DIFFRACTION100
3.1206-3.18820.36851350.26841212X-RAY DIFFRACTION100
3.1882-3.2620.30551370.25761236X-RAY DIFFRACTION100
3.262-3.34330.3041380.22811254X-RAY DIFFRACTION100
3.3433-3.43320.26131350.2211216X-RAY DIFFRACTION100
3.4332-3.53370.29151380.21491233X-RAY DIFFRACTION100
3.5337-3.64710.22951380.20491247X-RAY DIFFRACTION100
3.6471-3.77650.24381380.19731230X-RAY DIFFRACTION100
3.7765-3.92660.22361390.18121256X-RAY DIFFRACTION100
3.9266-4.10380.23381390.16631246X-RAY DIFFRACTION100
4.1038-4.31810.2271400.16991266X-RAY DIFFRACTION100
4.3181-4.58550.17671410.15131260X-RAY DIFFRACTION100
4.5855-4.93450.17631390.14131253X-RAY DIFFRACTION100
4.9345-5.42190.20321420.15181276X-RAY DIFFRACTION100
5.4219-6.18550.23891440.20411297X-RAY DIFFRACTION100
6.1855-7.7160.26291460.2341316X-RAY DIFFRACTION100
7.716-19.8320.22141540.19471380X-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)
13.38050.0672-0.7352.3551-1.42412.13360.1407-0.1816-0.0292-0.2313-0.0333-0.17060.02790.1580.00070.76180.06690.07060.46110.00530.689473.07390.7201103.2534
22.8088-0.1011-1.53621.21420.48263.9868-0.1245-0.03420.1289-0.14340.00640.10570.0117-0.09410.00020.7959-0.08060.03260.4850.00010.722873.328163.077897.5488
32.8799-0.0567-0.19312.88310.32852.48360.07440.2802-0.0691-0.3529-0.15690.3010.1237-0.92980.00010.8520.01170.03690.78540.01380.740157.49485.764496.7846
42.93960.60520.02312.3188-0.03762.8146-0.44-0.23360.36380.4060.78230.7302-0.4659-0.77150.02721.02510.5140.25631.1440.18310.967746.6511115.9858100.9651
52.84930.31540.30472.7035-1.35382.2420.1411-0.52910.44560.8935-0.18110.0751-1.1505-0.05390.00091.45880.2310.15870.7728-0.12590.823662.1548120.3606108.3719
63.80680.7591-0.62083.76430.07924.0217-0.00030.3842-0.1858-0.2386-0.22880.5905-0.127-0.91380.00170.698-0.0231-0.0320.956-0.06450.867449.463675.0577112.5901
73.69871.8034-1.58882.2591-1.40653.5350.1477-0.17920.2367-0.2974-0.01940.0571-0.3338-0.1704-0.00060.6384-0.02310.07490.7959-0.1290.726858.854188.5516133.698
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 29:139 )A29 - 139
2X-RAY DIFFRACTION2( CHAIN B AND RESID 27:138 )B27 - 138
3X-RAY DIFFRACTION3( CHAIN C AND RESID 28:138 )C28 - 138
4X-RAY DIFFRACTION4( CHAIN D AND RESID 28:137 )D28 - 137
5X-RAY DIFFRACTION5( CHAIN E AND RESID 28:142 )E28 - 142
6X-RAY DIFFRACTION6( CHAIN F AND RESID 27:139 )F27 - 139
7X-RAY DIFFRACTION7( CHAIN G AND RESID 28:139 )G28 - 139

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