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Yorodumi- PDB-1jyd: Crystal Structure of Recombinant Human Serum Retinol-Binding Prot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jyd | ||||||
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Title | Crystal Structure of Recombinant Human Serum Retinol-Binding Protein at 1.7 A Resolution | ||||||
Components | PLASMA RETINOL-BINDING PROTEIN | ||||||
Keywords | TRANSPORT PROTEIN / retinol binding protein / lipocalin superfamily / beta barrel | ||||||
Function / homology | Function and homology information Retinoid metabolism disease events / urinary bladder development / embryonic retina morphogenesis in camera-type eye / retinol transport / female genitalia morphogenesis / retinol transmembrane transporter activity / embryonic organ morphogenesis / maintenance of gastrointestinal epithelium / embryonic skeletal system development / negative regulation of cardiac muscle cell proliferation ...Retinoid metabolism disease events / urinary bladder development / embryonic retina morphogenesis in camera-type eye / retinol transport / female genitalia morphogenesis / retinol transmembrane transporter activity / embryonic organ morphogenesis / maintenance of gastrointestinal epithelium / embryonic skeletal system development / negative regulation of cardiac muscle cell proliferation / eye development / heart trabecula formation / cardiac muscle tissue development / retinal binding / retinol metabolic process / retinol binding / positive regulation of immunoglobulin production / Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / uterus development / vagina development / response to retinoic acid / Retinoid metabolism and transport / visual perception / gluconeogenesis / lung development / positive regulation of insulin secretion / glucose homeostasis / heart development / extracellular space / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Greene, L.H. / Chrysina, E.D. / Irons, L.I. / Papageorgiou, A.C. / Acharya, K.R. / Brew, K. | ||||||
Citation | Journal: Protein Sci. / Year: 2001 Title: Role of conserved residues in structure and stability: Tryptophans of human serum retinol-binding protein, a model for the lipocalin superfamily Authors: Greene, L.H. / Chrysina, E.D. / Irons, L.I. / Papageorgiou, A.C. / Acharya, K.R. / Brew, K. #1: Journal: Proteins / Year: 1990 Title: Crystallographic refinement of human serum retinol-binding protein at 2 A resolution Authors: Cowan, S.W. / Newcomer, M.E. / Jones, T.A. #2: Journal: J.Mol.Biol. / Year: 1993 Title: Crystal structure of the trigonal form of human plasma retinol-binding protein at 2.5 A resolution Authors: Zannotti, G. / Ottonello, S. / Berni, R. / Monaco, H.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jyd.cif.gz | 55 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jyd.ent.gz | 38.6 KB | Display | PDB format |
PDBx/mmJSON format | 1jyd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jy/1jyd ftp://data.pdbj.org/pub/pdb/validation_reports/jy/1jyd | HTTPS FTP |
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-Related structure data
Related structure data | 1jyjC 1rbpS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21115.645 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P02753 | ||
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#2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.47 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: Sodium cacodylate, sodium chloride, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 289K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.9 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→40 Å / Num. obs: 28189 / % possible obs: 90.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 23.1 Å2 / Rsym value: 0.047 / Net I/σ(I): 7.68 |
Reflection shell | Resolution: 1.7→1.72 Å / Mean I/σ(I) obs: 2.59 / Num. unique all: 1163 / Rsym value: 0.405 / % possible all: 91 |
Reflection | *PLUS Num. measured all: 67359 / Rmerge(I) obs: 0.047 |
Reflection shell | *PLUS Highest resolution: 1.7 Å / % possible obs: 91 % / Rmerge(I) obs: 0.505 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RBP Resolution: 1.7→19.15 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2348999.04 / Data cutoff high rms absF: 2348999.04 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.51 Å2 / ksol: 0.428 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 26.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→19.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 40 Å / Num. reflection obs: 27458 / % reflection Rfree: 5 % / Rfactor Rfree: 0.27 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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