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- PDB-4bxc: Resolving the activation site of positive regulators in plant pho... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4bxc | ||||||
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Title | Resolving the activation site of positive regulators in plant phosphoenolpyruvate carboxylase | ||||||
![]() | C4 PHOSPHOENOLPYRUVATE CARBOXYLASE | ||||||
![]() | LYASE / ALLOSTERIC REGULATION / C4 PHOTOSYNTHETIC PATHWAY / CO2 FIXATION / SULFATE BINDING SITE | ||||||
Function / homology | ![]() C4 photosynthesis / phosphoenolpyruvate carboxylase / phosphoenolpyruvate carboxylase activity / leaf development / carbon fixation / apoplast / tricarboxylic acid cycle / chloroplast / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schlieper, D. / Foerster, K. / Paulus, J.K. / Groth, G. | ||||||
![]() | ![]() Title: Resolving the Activation Site of Positive Regulators in Plant Phosphoenolpyruvate Carboxylase. Authors: Schlieper, D. / Foerster, K. / Paulus, J.K. / 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 | ![]() | 751.6 KB | Display | ![]() |
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PDB format | ![]() | 624.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 62.5 KB | Display | |
Data in CIF | ![]() | 85.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4bxhC ![]() 3zgeS 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
-Protein / Sugars , 2 types, 4 molecules AB![](data/chem/img/G6P.gif)
![](data/chem/img/G6P.gif)
#1: Protein | Mass: 113486.578 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P30694, phosphoenolpyruvate carboxylase #2: Sugar | |
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-Non-polymers , 4 types, 18 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-TRS / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 61 % / Description: NONE |
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Crystal grow | pH: 5.6 Details: 0.1 M TRI-SODIUM CITRATE (PH 5.6/NAOH), 15 % (W/V) PEG4000 AND 0.2 M AMMONIUM SULFATE; SOAKED WITH 200 MM GLUCOSE 6-PHOSPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.23953 Å / Relative weight: 1 |
Reflection | Resolution: 2.84→51.9 Å / Num. obs: 60347 / % possible obs: 99.7 % / Observed criterion σ(I): 1.9 / Redundancy: 6.6 % / Biso Wilson estimate: 74.3 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.84→2.99 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.9 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3ZGE Resolution: 2.86→50.68 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.936 / SU B: 29.512 / SU ML: 0.253 / Cross valid method: THROUGHOUT / ESU R: 2.487 / ESU R Free: 0.316 / 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 mean: 71.067 Å2
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Refinement step | Cycle: LAST / Resolution: 2.86→50.68 Å
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Refine LS restraints |
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