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Yorodumi- PDB-8qmv: L2 forming RubisCO derived from ancestral sequence reconstruction... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qmv | |||||||||
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Title | L2 forming RubisCO derived from ancestral sequence reconstruction of the last common ancestor of Form I'' and Form I RubisCOs | |||||||||
Components | RubisCO large subunit | |||||||||
Keywords | LYASE / RubisCO / CABP / ancestral | |||||||||
Function / homology | 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE Function and homology information | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | |||||||||
Authors | Zarzycki, J. / Schulz, L. / Erb, T.J. / Hochberg, G.K.A. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Biorxiv / Year: 2024 Title: Layered entrenchment maintains essentiality in the evolution of Form I Rubisco complexes Authors: Schulz, L. / Zarzycki, J. / Steinchen, W. / Hochberg, G.K.A. / Erb, T.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qmv.cif.gz | 728.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qmv.ent.gz | 606.3 KB | Display | PDB format |
PDBx/mmJSON format | 8qmv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qmv_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8qmv_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8qmv_validation.xml.gz | 84.4 KB | Display | |
Data in CIF | 8qmv_validation.cif.gz | 113.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qm/8qmv ftp://data.pdbj.org/pub/pdb/validation_reports/qm/8qmv | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 51155.840 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: ribulose-bisphosphate carboxylase #2: Sugar | ChemComp-CAP / #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | Has protein modification | Y | |
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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: 2.24 Å3/Da / Density % sol: 45 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Purified enzyme (10 mg/mL) in 25 mM Tricine-NaOH, 75 mM NaCl, pH 8.0 was incubated at 3% (v/v) CO2 in air and 30 degrees C for 1 hour in the presence of 0.3 mM CABP and 4.8 mM MgCl2. The ...Details: Purified enzyme (10 mg/mL) in 25 mM Tricine-NaOH, 75 mM NaCl, pH 8.0 was incubated at 3% (v/v) CO2 in air and 30 degrees C for 1 hour in the presence of 0.3 mM CABP and 4.8 mM MgCl2. The enzyme was then mixed in a 1:1 ratio with 0.1 M TRIS pH 8.5, 0.2 M magnesium chloride, 30 % (v/v) polyethylene glycol 400. The crystals were flash frozen in liquid nitrogen. |
-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: P14 (MX2) / Wavelength: 0.6888 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Dec 2, 2022 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.6888 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.85→24.97 Å / Num. obs: 155284 / % possible obs: 99.9 % / Redundancy: 13.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Rrim(I) all: 0.117 / Net I/σ(I): 16.04 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→24.97 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.98 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→24.97 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 17.8701 Å / Origin y: 58.0125 Å / Origin z: -19.673 Å
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Refinement TLS group | Selection details: all |