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- PDB-3rpz: Crystal Structure of ADP/ATP-dependent NAD(P)H-hydrate dehydratas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3rpz | ||||||
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Title | Crystal Structure of ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Bacillus subtilis co-crystallized with ATP/Mg2+ and soaked with NADPH | ||||||
![]() | ADP/ATP-dependent NAD(P)H-hydrate dehydratase | ||||||
![]() | lyase/lyase substrate / STRUCTURAL GENOMICS / PSI-biology / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG / LYASE / lyase-lyase substrate complex | ||||||
Function / homology | ![]() metabolite repair / ADP-dependent NAD(P)H-hydrate dehydratase / ADP-dependent NAD(P)H-hydrate dehydratase activity / NADHX epimerase activity / NADPHX epimerase activity / nicotinamide nucleotide metabolic process / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shumilin, I.A. / Cymborowski, M. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: Identification of unknown protein function using metabolite cocktail screening. Authors: Shumilin, I.A. / Cymborowski, M. / Chertihin, O. / Jha, K.N. / Herr, J.C. / Lesley, S.A. / Joachimiak, A. / Minor, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128.8 KB | Display | ![]() |
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PDB format | ![]() | 97.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3rnoC ![]() 3ro7C ![]() 3roeC ![]() 3rogC ![]() 3roxC ![]() 3rozC ![]() 3rphC ![]() 3rq2C ![]() 3rq5C ![]() 3rq6C ![]() 3rq8C ![]() 3rqhC ![]() 3rqqC ![]() 3rqxC ![]() 3rrbC ![]() 3rreC ![]() 3rrfC ![]() 3rrjC ![]() 3rs8C ![]() 3rs9C ![]() 3rsfC ![]() 3rsgC ![]() 3rsqC ![]() 3rssC ![]() 3rt7C ![]() 3rt9C ![]() 3rtaC ![]() 3rtbC ![]() 3rtcC ![]() 3rtdC ![]() 3rteC ![]() 3rtgC ![]() 3ru2C ![]() 3ru3C ![]() 1kyhS S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 30176.439 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P94368, ATP-dependent NAD(P)H-hydrate dehydratase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-AMP / |
#4: Chemical | ChemComp-NPW / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.005 M ATP, 0.18 M Magnesium Cloride, 13.5%(v/v) PEG 400, 10%(v/v) Glycerol, 0.09 M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 16, 2009 / Details: MIRRORS |
Diffraction measurement | Details: 1.00 degrees, 9.00 sec, detector distance 140.00 mm Method: scans |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Av R equivalents: 0.086 / Number: 281605 |
Reflection | Resolution: 1.51→50 Å / Num. obs: 57168 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 25.913 |
Cell measurement | Reflection used: 281605 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1KYH Resolution: 1.51→50 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.975 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 1.246 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, refinement counts Friedel's pair. U VALUES RESIDUAL ONLY
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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 max: 57.39 Å2 / Biso mean: 21.147 Å2 / Biso min: 11.13 Å2
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Refinement step | Cycle: LAST / Resolution: 1.51→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.51→1.549 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -0.308 Å / Origin y: -24.649 Å / Origin z: -23.727 Å
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