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- PDB-4lvc: Crystal structure of S-adenosyl-L-homocysteine hydrolase from Bra... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4lvc | ||||||
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Title | Crystal structure of S-adenosyl-L-homocysteine hydrolase from Bradyrhizobium elkanii in complex with adenosine | ||||||
![]() | S-adenosyl-L-homocysteine hydrolase (SAHase) | ||||||
![]() | HYDROLASE / cellular methylation / SAH hydrolysis / NAD+ cofactor / atmospheric nitrogen fixation / rhizobium-legume symbiosis / NAD+ cofactor complex | ||||||
Function / homology | ![]() adenosylhomocysteinase / adenosylhomocysteinase activity / S-adenosylmethionine cycle / one-carbon metabolic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Manszewski, T. / Singh, K. / Imiolczyk, B. / Jaskolski, M. | ||||||
![]() | ![]() Title: An enzyme captured in two conformational states: crystal structure of S-adenosyl-L-homocysteine hydrolase from Bradyrhizobium elkanii. Authors: Manszewski, T. / Singh, K. / Imiolczyk, B. / Jaskolski, M. #1: ![]() Title: High-resolution structures of complexes of plant S-adenosyl-L-homocysteine hydrolase (Lupinus luteus). Authors: Brzezinski, K. / Dauter, Z. / Jaskolski, M. #2: Journal: Acta Crystallogr.,Sect.F / Year: 2008 Title: Purification, crystallization and preliminary crystallographic studies of plant S-adenosyl-L-homocysteine hydrolase (Lupinus luteus). Authors: Brzezinski, K. / Bujacz, G. / Jaskolski, M. #3: ![]() Title: Crystal structure of S-adenosyl-L-homocysteine hydrolase from the human malaria parasite Plasmodium falciparum. Authors: Tanaka, N. / Nakanishi, M. / Kusakabe, Y. / Shiraiwa, K. / Yabe, S. / Ito, Y. / Kitade, Y. / Nakamura, K.T. #4: Journal: J.Biol.Chem. / Year: 1978 Title: Adenosylhomocysteine hydrolase. Crystallization of the purified enzyme and its properties. Authors: Richards, H.H. / Chiang, P.K. / Cantoni, G.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 792.1 KB | Display | ![]() |
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PDB format | ![]() | 656.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.4 MB | Display | ![]() |
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Full document | ![]() | 2.4 MB | Display | |
Data in XML | ![]() | 85.9 KB | Display | |
Data in CIF | ![]() | 127.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3n58S 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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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 52737.238 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0A087WNH6*PLUS, adenosylhomocysteinase |
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-Non-polymers , 6 types, 1732 molecules ![](data/chem/img/ADN.gif)
![](data/chem/img/NH4.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NH4.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-NAD / #5: Chemical | ChemComp-GOL / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.64 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.1 Details: 0.2 M ammonium acetate, pH 7.1, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Apr 26, 2011 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Number: 1278402 / Rmerge(I) obs: 0.086 / D res high: 1.74 Å / Num. obs: 200550 / % possible obs: 98.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.74→47.85 Å / Num. all: 203245 / Num. obs: 200550 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 6.37 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 12.34 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3N58 Resolution: 1.74→47.85 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 4.279 / SU ML: 0.063 / SU R Cruickshank DPI: 0.0925 / Cross valid method: R-FREE / ESU R: 0.091 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: Hydrogen atoms were added at riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.592 Å2
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Refinement step | Cycle: LAST / Resolution: 1.74→47.85 Å
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Refine LS restraints |
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