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- PDB-7ocp: NADPH bound to the dehydrogenase domain of the bifunctional manni... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ocp | ||||||
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Title | NADPH bound to the dehydrogenase domain of the bifunctional mannitol-1-phosphate dehydrogenase/phosphatase MtlD from Acinetobacter baumannii | ||||||
![]() | HAD hydrolase, family IA, variant 3 | ||||||
![]() | OXIDOREDUCTASE / Mannitol / Dehydrogenase / Phosphatase / NADPH / Fructose-6-phosphate / HAD hydrolase family IA variant 3 | ||||||
Function / homology | ![]() oxidoreductase activity / hydrolase activity / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tam, H.K. / Mueller, V. / Pos, K.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Unidirectional mannitol synthesis of Acinetobacter baumannii MtlD is facilitated by the helix-loop-helix-mediated dimer formation. Authors: Tam, H.K. / Konig, P. / Himpich, S. / Ngu, N.D. / Abele, R. / Muller, V. / Pos, K.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 569 KB | Display | ![]() |
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PDB format | ![]() | 475.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 47 KB | Display | |
Data in CIF | ![]() | 63.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ocnSC ![]() 7ocqC ![]() 7ocrC ![]() 7ocsC ![]() 7octC ![]() 7ocuC 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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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 83548.258 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81 Gene: HMPREF0010_00722 / Plasmid: pET21 / Production host: ![]() ![]() |
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-Non-polymers , 7 types, 47 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NDP.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NDP.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-EDO / | ||||||||||
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#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-EPE / | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.2 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M BIS-Tris propane pH6.5, 0.2M Na2SO4, 14% PEG3350, 0.02M MgCl2, 0.1M Potassium acetate with microseeding |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 22, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.75→48.59 Å / Num. obs: 45271 / % possible obs: 100 % / Redundancy: 12.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.038 / Rrim(I) all: 0.135 / Net I/σ(I): 13.4 / Num. measured all: 550329 / Scaling rejects: 85 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7OCN Resolution: 2.75→48.59 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.929 / SU B: 43.456 / SU ML: 0.372 / SU R Cruickshank DPI: 0.3353 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.364 / 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 max: 213.65 Å2 / Biso mean: 90.895 Å2 / Biso min: 39.8 Å2
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Refinement step | Cycle: final / Resolution: 2.75→48.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.821 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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