+Open data
-Basic information
Entry | Database: PDB / ID: 7naz | ||||||
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Title | TPR-rich domain of EccA3 from M. smegmatis | ||||||
Components | ESX-3 secretion system protein EccA3 | ||||||
Keywords | UNKNOWN FUNCTION / EccA / Type VII Secretion | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mycolicibacterium smegmatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å | ||||||
Authors | Crosskey, T.D. / Wilmanns, M. | ||||||
Citation | Journal: To Be Published Title: Structure of TPR-rich domain of M. smegmatis EccA3 Authors: Crosskey, T.D. / Wilmanns, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7naz.cif.gz | 132.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7naz.ent.gz | 108.3 KB | Display | PDB format |
PDBx/mmJSON format | 7naz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/na/7naz ftp://data.pdbj.org/pub/pdb/validation_reports/na/7naz | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32268.959 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / Gene: eccA3, MSMEG_0615, MSMEI_0599 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0QQ38 | ||||||||
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#2: Chemical | ChemComp-DIO / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.34 Å3/Da / Density % sol: 63.16 % |
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Crystal grow | Temperature: 292.15 K / Method: vapor diffusion / pH: 6.5 Details: 0.1 M MES pH6.5, 10 %(v/v) dioxane, 1.6 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976241 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 13, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976241 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→45.94 Å / Num. obs: 53900 / % possible obs: 100 % / Redundancy: 10 % / Biso Wilson estimate: 22.38 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.027 / Rrim(I) all: 0.071 / Χ2: 0.93 / Net I/av σ(I): 18.7 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 1.42→1.44 Å / Num. unique obs: 75904 / CC1/2: 0.997 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.6→45.94 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.97 / SU B: 3.106 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.3 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.017 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→45.94 Å
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