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Yorodumi- PDB-4nh0: Cytoplasmic domain of the Thermomonospora curvata Type VII Secret... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nh0 | ||||||
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Title | Cytoplasmic domain of the Thermomonospora curvata Type VII Secretion ATPase EccC | ||||||
Components | Cell divisionFtsK/SpoIIIE | ||||||
Keywords | CELL CYCLE / ATPase / secretion / EsxB | ||||||
Function / homology | Function and homology information localization / ATP hydrolysis activity / DNA binding / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Thermomonospora curvata (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.9 Å | ||||||
Authors | Rosenberg, O.S. / Cox, J.S. / Stroud, R.M. / Strauli, N. / Dovala, D. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2015 Title: Substrates Control Multimerization and Activation of the Multi-Domain ATPase Motor of Type VII Secretion. Authors: Rosenberg, O.S. / Dovala, D. / Li, X. / Connolly, L. / Bendebury, A. / Finer-Moore, J. / Holton, J. / Cheng, Y. / Stroud, R.M. / Cox, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nh0.cif.gz | 362 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nh0.ent.gz | 279.7 KB | Display | PDB format |
PDBx/mmJSON format | 4nh0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nh0_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 4nh0_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 4nh0_validation.xml.gz | 60.8 KB | Display | |
Data in CIF | 4nh0_validation.cif.gz | 81.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nh/4nh0 ftp://data.pdbj.org/pub/pdb/validation_reports/nh/4nh0 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 126474.375 Da / Num. of mol.: 2 Fragment: Cytoplasmic domain of EccC ATPase, UNP residues 200-1315 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermomonospora curvata (bacteria) / Strain: ATCC 19995 / DSM 43183 / JCM 3096 / NCIMB 10081 / Gene: Tcur_0607 / Production host: Escherichia coli (E. coli) / References: UniProt: D1A4G7 #2: Chemical | #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-ATP / #5: 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: 4.92 Å3/Da / Density % sol: 74.98 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: EccCTc(199-1315) was concentrated to 14 mg/ml and adjusted 10 mM ATP from a 100 mM stock (Roche). The protein was mixed with a 1:1 volume of 0.1 M Tris pH 8.0, 0.6-1.1 M (NH4)2SO4, 0.1 M ...Details: EccCTc(199-1315) was concentrated to 14 mg/ml and adjusted 10 mM ATP from a 100 mM stock (Roche). The protein was mixed with a 1:1 volume of 0.1 M Tris pH 8.0, 0.6-1.1 M (NH4)2SO4, 0.1 M glycine, 0.020 mM MgCl2, 0.1 M NaCl,, equilibrated in a vapor diffusion experiment at 20 C over 500 mL of the mother liquor., VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9796 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 5, 2012 |
Radiation | Monochromator: Cryo-Cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→48.93 Å / Num. obs: 108032 / Redundancy: 6.9 % / Rsym value: 0.1416 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 0.58 / Num. unique all: 10657 / Rsym value: 0.02235 / % possible all: 98.72 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.9→48.93 Å / SU ML: 0.53 / σ(F): 1.34 / Phase error: 32.09 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→48.93 Å
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Refine LS restraints |
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LS refinement shell |
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