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- PDB-7x2y: Crystal Structure of cis-4,5-dihydrodiol phthalate dehydrogenase ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7x2y | ||||||
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Title | Crystal Structure of cis-4,5-dihydrodiol phthalate dehydrogenase in complex with NAD+ and 3-Hydroxybenzoate | ||||||
![]() | 4,5-dihydroxyphthalate dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / dehydrogenase / bacterial protein / NAD cofactor | ||||||
Function / homology | 3-HYDROXYBENZOIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Sharma, M. / Mahto, J.K. / Kumar, P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Conformational flexibility enables catalysis of phthalate cis-4,5-dihydrodiol dehydrogenase. Authors: Mahto, J.K. / Sharma, M. / Neetu, N. / Kayastha, A. / Aggarwal, S. / Kumar, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 160.2 KB | Display | ![]() |
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PDB format | ![]() | 122.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 34.6 KB | Display | |
Data in CIF | ![]() | 47.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7wzdC ![]() 7x1xC ![]() 3moiS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 4 - 391 / Label seq-ID: 4 - 391
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 43046.676 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 351 molecules ![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/3HB.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/3HB.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PEG / #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M Ammonium phosphate dibasic, and 20 % polyethylene glycol 3350, 100 mM Tris buffer pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Dec 13, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.48→27.18 Å / Num. obs: 28203 / % possible obs: 99.8 % / Redundancy: 6.8 % / CC1/2: 0.994 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.48→2.54 Å / Num. unique obs: 3138 / CC1/2: 0.904 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3MOI Resolution: 2.48→27.18 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.919 / SU B: 8.844 / SU ML: 0.197 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.646 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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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: 137.95 Å2 / Biso mean: 21.005 Å2 / Biso min: 0.86 Å2
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Refinement step | Cycle: final / Resolution: 2.48→27.18 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 11307 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.48→2.544 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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