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Yorodumi- PDB-4nss: A structural and functional investigation of a novel protein from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nss | ||||||
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Title | A structural and functional investigation of a novel protein from Mycobacterium smegmatis implicated in mycobacterial macrophage survivability | ||||||
Components | Mycobacterial protein | ||||||
Keywords | UNKNOWN FUNCTION / Mycobacterial survival | ||||||
Function / homology | Nonspecific Lipid-transfer Protein; Chain A - #40 / Bacterial SCP orthologue / Bacterial SCP ortholog / Nonspecific Lipid-transfer Protein; Chain A / 2-Layer Sandwich / Alpha Beta / Bacterial SCP orthologue domain-containing protein Function and homology information | ||||||
Biological species | Mycobacterium smegmatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Shahine, A.E. / Littler, D. / Brammananath, R. / Chan, P.Y. / Crellin, P.K. / Coppel, R.L. / Rossjohn, J. / Beddoe, T. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: A structural and functional investigation of a novel protein from Mycobacterium smegmatis implicated in mycobacterial macrophage survivability. Authors: Shahine, A. / Littler, D. / Brammananath, R. / Chan, P.Y. / Crellin, P.K. / Coppel, R.L. / Rossjohn, J. / Beddoe, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nss.cif.gz | 98.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nss.ent.gz | 77.5 KB | Display | PDB format |
PDBx/mmJSON format | 4nss.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nss_validation.pdf.gz | 451 KB | Display | wwPDB validaton report |
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Full document | 4nss_full_validation.pdf.gz | 451.4 KB | Display | |
Data in XML | 4nss_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 4nss_validation.cif.gz | 13.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ns/4nss ftp://data.pdbj.org/pub/pdb/validation_reports/ns/4nss | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15668.760 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_5817, MSMEI_5660 / Production host: Escherichia coli (E. coli) / References: UniProt: A0R4F7 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.7 Details: 1.42M Lithium Sulfate, 0.1M Tris HCl pH 7.7, 0.1M sodium citrate tribasic dihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 26, 2011 |
Radiation | Monochromator: SYNCHROTRON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95369 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50.05 Å / Num. obs: 10787 / % possible obs: 98.7 % / Observed criterion σ(F): 1.65 / Biso Wilson estimate: 53.67 Å2 |
Reflection shell | Resolution: 2.4→2.67 Å / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→40.42 Å / Cor.coef. Fo:Fc: 0.9449 / Cor.coef. Fo:Fc free: 0.9156 / SU R Cruickshank DPI: 0.309 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 61.39 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→40.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.68 Å / Total num. of bins used: 5
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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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