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Yorodumi- PDB-6hzk: Crystal structure of redox-inhibited phosphoribulokinase from Syn... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hzk | ||||||
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Title | Crystal structure of redox-inhibited phosphoribulokinase from Synechococcus sp. (strain PCC 6301) | ||||||
Components | Phosphoribulokinase | ||||||
Keywords | TRANSFERASE / Phosphoribulokinase / Calvin cycle | ||||||
Function / homology | Function and homology information phosphoribulokinase / phosphoribulokinase activity / carbohydrate metabolic process / phosphorylation / ATP binding Similarity search - Function | ||||||
Biological species | Synechococcus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å | ||||||
Authors | Wilson, R.H. / Bracher, A. / Hartl, F.U. / Hayer-Hartl, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2019 Title: Crystal structure of phosphoribulokinase from Synechococcus sp. strain PCC 6301. Authors: Wilson, R.H. / Hayer-Hartl, M. / Bracher, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hzk.cif.gz | 260.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hzk.ent.gz | 213.1 KB | Display | PDB format |
PDBx/mmJSON format | 6hzk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hz/6hzk ftp://data.pdbj.org/pub/pdb/validation_reports/hz/6hzk | HTTPS FTP |
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-Related structure data
Related structure data | 6hzlSC 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 0 / Auth seq-ID: 4 - 332 / Label seq-ID: 4 - 332
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-Components
#1: Protein | Mass: 37760.750 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1) (bacteria) Gene: prk, syc0567_d / Plasmid: pHUE-prk4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3K6J7, phosphoribulokinase #2: 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: 2.6 Å3/Da / Density % sol: 52.67 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 8 / Details: 20 % PEG-3350, 200 mM ammonium fluoride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0332 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→49.12 Å / Num. obs: 30873 / % possible obs: 99.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 62.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.034 / Rrim(I) all: 0.081 / Net I/σ(I): 12 / Num. measured all: 171405 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.544
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: preliminary version of 6HZL Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.2521 / WRfactor Rwork: 0.2157 / FOM work R set: 0.75 / SU B: 25.046 / SU ML: 0.252 / SU R Cruickshank DPI: 0.3942 / SU Rfree: 0.2583 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.394 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 235.7 Å2 / Biso mean: 99.671 Å2 / Biso min: 43.03 Å2
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Refinement step | Cycle: final / Resolution: 2.4→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 18139 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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