+Open data
-Basic information
Entry | Database: PDB / ID: 6nop | ||||||
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Title | Structure of Cyanothece McdA(D38A)-ATP complex | ||||||
Components | Cobyrinic acid ac-diamide synthase | ||||||
Keywords | DNA BINDING PROTEIN / McdA / McdB / carboxysome / segregation / nucleoid DNA / Walker box / novel signature lysine | ||||||
Function / homology | AAA domain / AAA domain / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / P-loop containing nucleoside triphosphate hydrolase / ADENOSINE-5'-TRIPHOSPHATE / Maintenance of carboxysome distribution protein A Function and homology information | ||||||
Biological species | Cyanothece (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å | ||||||
Authors | Schumacher, M.A. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2019 Title: Structures of maintenance of carboxysome distribution Walker-box McdA and McdB adaptor homologs. Authors: Schumacher, M.A. / Henderson, M. / Zhang, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nop.cif.gz | 220.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nop.ent.gz | 174.2 KB | Display | PDB format |
PDBx/mmJSON format | 6nop.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/no/6nop ftp://data.pdbj.org/pub/pdb/validation_reports/no/6nop | HTTPS FTP |
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-Related structure data
Related structure data | 6nonSC 6nooC 6noyC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29871.238 Da / Num. of mol.: 2 / Mutation: D38A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cyanothece (bacteria) / Gene: PCC7424_5529 / Production host: Escherichia coli (E. coli) / References: UniProt: B7KMS4 #2: Chemical | #3: Chemical | #4: 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: 2.47 Å3/Da / Density % sol: 50.27 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: Peg 400, 0.1 M phosphate buffer |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→76.65 Å / Num. obs: 60006 / % possible obs: 92.3 % / Redundancy: 6.4 % / CC1/2: 1 / Rpim(I) all: 0.01 / Rsym value: 0.026 / Net I/σ(I): 31 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 3959 / CC1/2: 0.903 / Rpim(I) all: 0.263 / Rsym value: 0.379 / % possible all: 80.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6NON Resolution: 1.7→60.87 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.09
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Bsol: 64.166 Å2 / ksol: 0.373 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 157.92 Å2 / Biso mean: 44.41 Å2 / Biso min: 21.93 Å2
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Refinement step | Cycle: final / Resolution: 1.7→60.87 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Origin x: -39.6962 Å / Origin y: 17.0273 Å / Origin z: -37.9031 Å
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Refinement TLS group |
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