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- PDB-3roe: 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: 3roe | ||||||
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Title | Crystal Structure of Mouse Apolipoprotein A-I Binding Protein in Complex with Thymidine | ||||||
![]() | 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 | ![]() | 554.5 KB | Display | ![]() |
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PDB format | ![]() | 462.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 501.3 KB | Display | ![]() |
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Full document | ![]() | 522.9 KB | Display | |
Data in XML | ![]() | 56.6 KB | Display | |
Data in CIF | ![]() | 77.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3rnoC ![]() 3ro7C ![]() 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.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-THM / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.36 % |
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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 / Detector: CCD / Date: Nov 22, 2008 / Details: MIRRORS |
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: 0.087 / Number: 477756 |
Reflection | Resolution: 2.11→50 Å / Num. all: 477756 / Num. obs: 477756 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 26.826 |
Reflection shell | Resolution: 2.11→2.15 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.593 / Mean I/σ(I) obs: 2.568 / Rsym value: 0.593 / % possible all: 83.3 |
Cell measurement | Reflection used: 477756 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2O8N Resolution: 2.11→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.572 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 34.638 Å2
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Refinement step | Cycle: LAST / Resolution: 2.11→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.11→2.165 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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