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- PDB-3zgb: Greater efficiency of photosynthetic carbon fixation due to singl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3zgb | ||||||
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Title | Greater efficiency of photosynthetic carbon fixation due to single amino acid substitution | ||||||
![]() | PHOSPHOENOLPYRUVATE CARBOXYLASE | ||||||
![]() | LYASE | ||||||
Function / homology | ![]() phosphoenolpyruvate carboxylase / phosphoenolpyruvate carboxylase activity / carbon fixation / photosynthesis / tricarboxylic acid cycle / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Paulus, J.K. / Schlieper, D. / Groth, G. | ||||||
![]() | ![]() Title: Greater Efficiency of Photosynthetic Carbon Fixation due to Single Amino Acid Substitution Authors: Paulus, J.K. / Schlieper, D. / Groth, G. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 730.8 KB | Display | ![]() |
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PDB format | ![]() | 608.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 486.3 KB | Display | ![]() |
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Full document | ![]() | 509.2 KB | Display | |
Data in XML | ![]() | 61.8 KB | Display | |
Data in CIF | ![]() | 85.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3zgeC ![]() 3zbeS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 111472.367 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: THE GENE NAME OF THE PROTEIN IS PPCA / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q01647, phosphoenolpyruvate carboxylase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Sequence details | THE CRYSTALLIZED SEQUENCE ACTUALLY MAPS TO NCBI ACCESSION CODE Z48966 WITHOUT ANY CONFLICTS OR GAPS. ...THE CRYSTALLIZ | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61 % / Description: NONE |
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Crystal grow | pH: 5.6 Details: 0.2 M AMMONIUM SULFATE, 0.1 M TRI-SODIUM CITRATE/HCL PH 5.6, 10 % (W/V) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 27, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12678 Å / Relative weight: 1 |
Reflection | Resolution: 2.71→165.55 Å / Num. obs: 71548 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 15.8 % / Biso Wilson estimate: 55.8 Å2 / Rsym value: 0.099 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 2.71→2.86 Å / Redundancy: 16.4 % / Mean I/σ(I) obs: 2 / Rsym value: 0.334 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3ZBE Resolution: 2.71→78.72 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.918 / SU B: 21.152 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.567 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.58 Å2
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Refinement step | Cycle: LAST / Resolution: 2.71→78.72 Å
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Refine LS restraints |
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