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Yorodumi- PDB-1eta: THE X-RAY CRYSTAL STRUCTURE REFINEMENTS OF NORMAL HUMAN TRANSTHYR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1eta | |||||||||
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Title | THE X-RAY CRYSTAL STRUCTURE REFINEMENTS OF NORMAL HUMAN TRANSTHYRETIN AND THE AMYLOIDOGENIC VAL 30-->MET VARIANT TO 1.7 ANGSTROMS RESOLUTION | |||||||||
Components | TRANSTHYRETIN | |||||||||
Keywords | TRANSPORT(THYROXINE) | |||||||||
Function / homology | Function and homology information Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation ...Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.7 Å | |||||||||
Authors | Braden, B.C. / Steinrauf, L.K. / Hamilton, J.A. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 1993 Title: The x-ray crystal structure refinements of normal human transthyretin and the amyloidogenic Val-30-->Met variant to 1.7-A resolution. Authors: Hamilton, J.A. / Steinrauf, L.K. / Braden, B.C. / Liepnieks, J. / Benson, M.D. / Holmgren, G. / Sandgren, O. / Steen, L. #1: Journal: J.Biol.Chem. / Year: 1993 Title: X-Ray Crystal Structure of the Ala 109-->Thr Variant of Human Transthyretin which Produces Euthyroid Hyperthyroxinemia Authors: Steinrauf, L.K. / Hamilton, J.A. / Braden, B.C. / Murrell, J.R. / Benson, M.D. #2: Journal: Biochim.Biophys.Acta / Year: 1992 Title: Alteration in Molecular Structure which Results in Disease: The met 30 Variant of Human Plasma Transthyretin Authors: Hamilton, J.A. / Steinrauf, L.K. / Liepnieks, J.J. / Benson, M.D. / Holmgren, G. / Sandgren, O. / Steen, L. | |||||||||
History |
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Remark 700 | SHEET SHEET IDENTIFIERS ARE BASED ON ENTRY 2PAB (PREALBUMIN, BLAKE ET AL.). A SHIFT OF THE CHAIN 1 ...SHEET SHEET IDENTIFIERS ARE BASED ON ENTRY 2PAB (PREALBUMIN, BLAKE ET AL.). A SHIFT OF THE CHAIN 1 AND 2 BETA SHEETS AT RESIDUE 30 WAS NECESSARY TO MODEL THE MET SIDE CHAIN. BETA SHEET MAIN CHAIN CONNECTIVITIES IN THE COORDINATE SET ARE TO THE VAL 30 PEPTIDE ATOMS. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1eta.cif.gz | 69.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1eta.ent.gz | 51.8 KB | Display | PDB format |
PDBx/mmJSON format | 1eta.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1eta_validation.pdf.gz | 965 KB | Display | wwPDB validaton report |
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Full document | 1eta_full_validation.pdf.gz | 984.7 KB | Display | |
Data in XML | 1eta_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 1eta_validation.cif.gz | 25.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/et/1eta ftp://data.pdbj.org/pub/pdb/validation_reports/et/1eta | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Atom site foot note | 1: THIS IS A NATURALLY OCCURRING VARIANT WITH MICROHETEROGENEITY AT POSITION 30. BOTH VAL AND MET OCCUR AT THIS POSITION. THE RATIO OF MET VAL AT POSITION 30 IS 1:1 AND BOTH VAL AND MET ARE MODELLED WITH 0.50 OCCUPANCY. | ||||||||
Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.9886, 0.1508, -0.0004), Vector: Details | THERE ARE TWO T4 BINDING SITES PER TETRAMER (AA, BB). SITE AA CONTAINS RESIDUES FROM CHAIN 1 AND CHAIN 1* WHERE CHAINS 1 AND 1* ARE RELATED BY CRYSTALLOGRAPHIC TWO-FOLD SYMMETRY. LIKEWISE, SITE BB CONTAINS RESIDUES FROM CHAIN 2 AND CHAIN 2* WHERE CHAINS 2 AND 2* ARE RELATED BY CRYSTALLOGRAPHIC SYMMETRY. BECAUSE OF PDB FORMAT SPECIFICATIONS, ONLY THE RESIDUES FROM CHAIN 1 ARE LISTED FOR SITE AA ON SITE RECORDS BELOW AND ONLY THE RESIDUES FROM CHAIN 2 ARE LISTED FOR SITE BB ON SITE RECORDS BELOW. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN 2 WHEN APPLIED TO CHAIN 1. | |
-Components
#1: Protein | Mass: 13809.426 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: SERUM / References: UniProt: P02766 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.02 % |
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Crystal grow | *PLUS Method: unknown |
-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
-Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.7→5 Å / Rfactor obs: 0.184 / σ(F): 2 Details: OCCUPANCIES OF DISORDERED SIDE CHAINS OR OF ATOMS WITH LESS THAN UNIT OCCUPANCY WERE SELECTED TO FLATTEN THE FINAL DIFFERENCE FOURIER. OCCUPANCIES OF SOLVENT WATER MOLECULES WERE REFINED ...Details: OCCUPANCIES OF DISORDERED SIDE CHAINS OR OF ATOMS WITH LESS THAN UNIT OCCUPANCY WERE SELECTED TO FLATTEN THE FINAL DIFFERENCE FOURIER. OCCUPANCIES OF SOLVENT WATER MOLECULES WERE REFINED WITH PROLSQ. OCCUPANCIES OF DISORDERED SIDE CHAINS OR OF ATOMS WITH LESS THAN UNIT OCCUPANCY WERE SELECTED TO FLATTEN THE FINAL DIFFERENCE FOURIER. ATOMS WITH OCCUPANCIES OF .001 HAVE NO OBSERVABLE ELECTRON DENSITY. SOME WATER MOLECULES WERE PLACED IN POSITIONS THAT PROBABLY REPRESENT ALTERNATE CONFORMATIONS. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→5 Å
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Refine LS restraints |
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Refine LS restraints | *PLUS Type: p_angle_d / Dev ideal: 0.027 |