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Open data
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Basic information
Entry | Database: PDB / ID: 4zjm | ||||||||||||
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Title | Crystal Structure of Mycobacterium tuberculosis LpqH (Rv3763) | ||||||||||||
![]() | (Lipoprotein LpqH) x 7 | ||||||||||||
![]() | UNKNOWN FUNCTION / lipoprotein / virulence / structural genomics / PSI-2 / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC | ||||||||||||
Function / homology | ![]() symbiont-mediated perturbation of host immune response / symbiont-mediated activation of host apoptosis / bacterial extracellular vesicle / biological process involved in interaction with host / peptidoglycan-based cell wall / host cell cytoplasm / host cell surface receptor binding / defense response to bacterium / cell surface / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Arbing, M.A. / Chan, S. / Kuo, E. / Harris, L.R. / Zhou, T.T. / Eisenberg, D. / TB Structural Genomics Consortium (TBSGC) | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 290.3 KB | Display | ![]() |
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PDB format | ![]() | 238.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 519.2 KB | Display | ![]() |
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Full document | ![]() | 530 KB | Display | |
Data in XML | ![]() | 29 KB | Display | |
Data in CIF | ![]() | 39.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4xinS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
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Components
-Protein , 7 types, 7 molecules ABCDEFG
#1: Protein | Mass: 11956.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 25618 / H37Rv / Gene: lpqH, Rv3763, MTV025.111 / Plasmid: pMAPLe3 / Details (production host): pET28 derivative / Production host: ![]() ![]() |
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#2: Protein | Mass: 11902.143 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() 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 | Mass: 11875.097 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() 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 | Mass: 11875.097 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() 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 | Mass: 11902.143 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() 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 | Mass: 11902.143 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() 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 | Mass: 11929.189 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() 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 |
-Non-polymers , 4 types, 39 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#8: Chemical | ChemComp-SO4 / #9: Chemical | #10: Chemical | ChemComp-CL / | #11: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.63 Å3/Da / Density % sol: 66.13 % |
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Crystal grow | Temperature: 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. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 25, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
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Refinement | Method to determine structure: ![]() Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 86.4885 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.851→19.832 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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