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- PDB-3rno: Crystal Structure of Mouse Apolipoprotein A-I Binding Protein in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3rno | ||||||
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Title | Crystal Structure of Mouse Apolipoprotein A-I Binding Protein in Complex with NADP. | ||||||
![]() | Apolipoprotein A-I-binding protein | ||||||
![]() | PROTEIN BINDING / ROSSMANN FOLD | ||||||
Function / homology | ![]() membrane raft distribution / NAD(P)H-hydrate epimerase / NADHX epimerase activity / NADPHX epimerase activity / regulation of cholesterol efflux / nicotinamide nucleotide metabolic process / Nicotinamide salvaging / sprouting angiogenesis / lipid transport / negative regulation of angiogenesis ...membrane raft distribution / NAD(P)H-hydrate epimerase / NADHX epimerase activity / NADPHX epimerase activity / regulation of cholesterol efflux / nicotinamide nucleotide metabolic process / Nicotinamide salvaging / sprouting angiogenesis / lipid transport / negative regulation of angiogenesis / cilium / cell body / nucleotide binding / mitochondrion / extracellular space / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shumilin, I.A. / Jha, K.N. / Cymborowski, M. / Herr, J.C. / Minor, W. | ||||||
![]() | ![]() 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 | ![]() | 108.9 KB | Display | ![]() |
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PDB format | ![]() | 83.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 752.7 KB | Display | ![]() |
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Full document | ![]() | 755.3 KB | Display | |
Data in XML | ![]() | 10.8 KB | Display | |
Data in CIF | ![]() | 13.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ro7C ![]() 3roeC ![]() 3rogC ![]() 3roxC ![]() 3rozC ![]() 3rphC ![]() 3rpzC ![]() 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 ![]() 2o8nS S: Starting model for refinement C: citing same article ( |
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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
#1: Protein | Mass: 29872.963 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-NAP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1 M SODIUM ACETATE, 1.5 M AMMONIUM SULFATE, PH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 22, 2008 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12712 Å / Relative weight: 1 |
Reflection | Av R equivalents: 0.097 / Number: 108351 |
Reflection | Resolution: 2.5→50 Å / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.2 % / Biso Wilson estimate: 53.3 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 41.2 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 2.846 / Rsym value: 0.537 / % possible all: 89.5 |
Cell measurement | Reflection used: 108351 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2o8n Resolution: 2.5→48.63 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / Occupancy max: 1 / Occupancy min: 1 / SU B: 17.01 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; 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: 125.07 Å2 / Biso mean: 59.071 Å2 / Biso min: 17.51 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→48.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / 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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