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Yorodumi- PDB-5nvd: Crystal structure of hexameric CBS-CP12 protein from bloom-formin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nvd | ||||||
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Title | Crystal structure of hexameric CBS-CP12 protein from bloom-forming cyanobacteria at 2.5 A resolution in P6322 crystal form | ||||||
Components | CBS-CP12 | ||||||
Keywords | PHOTOSYNTHESIS / Cystathionine beta synthase domain / fusion protein / redox-regulation of photosynthesis | ||||||
Function / homology | CP12 domain / CP12 domain / CP12 / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Similar to tr Function and homology information | ||||||
Biological species | Microcystis aeruginosa PCC 7806 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Hackenberg, C. / Hakanpaa, J. / Eigner, C. / Antonyuk, S.V. / Dittmann, E. / Lamzin, V.S. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 Title: Structural and functional insights into the unique CBS-CP12 fusion protein family in cyanobacteria. Authors: Hackenberg, C. / Hakanpaa, J. / Cai, F. / Antonyuk, S. / Eigner, C. / Meissner, S. / Laitaoja, M. / Janis, J. / Kerfeld, C.A. / Dittmann, E. / Lamzin, V.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nvd.cif.gz | 84.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nvd.ent.gz | 62.9 KB | Display | PDB format |
PDBx/mmJSON format | 5nvd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nv/5nvd ftp://data.pdbj.org/pub/pdb/validation_reports/nv/5nvd | HTTPS FTP |
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-Related structure data
Related structure data | 5nmuSC 5nplC 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: 23154.561 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: First four residues in the sequence are EXPRESSION TAG Source: (gene. exp.) Microcystis aeruginosa PCC 7806 (bacteria) Gene: IPF_2164 / Production host: Escherichia coli (E. coli) / Strain (production host): LOBSTR / References: UniProt: A8YJ50 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 60 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Protein at 6.08 mg/ml in 50 mM Bicine/KOH pH 7.8, 40 mM KCl, 0.132 mM AMP solution was mixed with reservoir solution containing 0.15 M KSCN, 0.1 M HEPES pH 7.0 and 18% PEG3350 containing 0.1 ...Details: Protein at 6.08 mg/ml in 50 mM Bicine/KOH pH 7.8, 40 mM KCl, 0.132 mM AMP solution was mixed with reservoir solution containing 0.15 M KSCN, 0.1 M HEPES pH 7.0 and 18% PEG3350 containing 0.1 mM Guanidine hydrochloride. Cryoprotector - reservoir solution with 25% ethylene glycol. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→100.62 Å / Num. obs: 10477 / % possible obs: 99.9 % / Redundancy: 18.5 % / Biso Wilson estimate: 59.721 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.027 / Net I/σ(I): 23.4 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 17.6 % / Rmerge(I) obs: 1.354 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1142 / CC1/2: 0.881 / Rpim(I) all: 0.462 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5NMU Resolution: 2.5→85.07 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.937 / SU B: 20.157 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.284 / ESU R Free: 0.223 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 74.6 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→85.07 Å
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