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Yorodumi- PDB-1mol: TWO CRYSTAL STRUCTURES OF A POTENTLY SWEET PROTEIN: NATURAL MONEL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mol | ||||||
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Title | TWO CRYSTAL STRUCTURES OF A POTENTLY SWEET PROTEIN: NATURAL MONELLIN AT 2.75 ANGSTROMS RESOLUTION AND SINGLE-CHAIN MONELLIN AT 1.7 ANGSTROMS RESOLUTION | ||||||
Components | MONELLIN | ||||||
Keywords | SWEET-TASTING PROTEIN | ||||||
Function / homology | Monellin, B chain / Monellin / Monellin / Nuclear Transport Factor 2; Chain: A, - #10 / Cystatin superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / Monellin chain B Function and homology information | ||||||
Biological species | Dioscoreophyllum cumminsii (serendipity berry) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.7 Å | ||||||
Authors | Somoza, J.R. / Kim, S.-H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1993 Title: Two crystal structures of a potently sweet protein. Natural monellin at 2.75 A resolution and single-chain monellin at 1.7 A resolution. Authors: Somoza, J.R. / Jiang, F. / Tong, L. / Kang, C.H. / Cho, J.M. / Kim, S.H. #1: Journal: J.Biomol.NMR / Year: 1992 Title: 1H Resonance Assignments, Secondary Structure and General Topology of Single-Chain Monellin in Solution as Determined by 1H-2D-NMR Authors: Tomic, M.T. / Somoza, J.R. / Wemmer, D.E. / Park, Y.W. / Cho, J.M. / Kim, S.-H. #2: Journal: Protein Eng. / Year: 1989 Title: Redesigning a Sweet Protein: Increased Stability and Renaturability Authors: Kim, S.-H. / Kang, C.-H. / Kim, R. / Cho, J.M. / Lee, Y.-B. / Lee, T.-K. | ||||||
History |
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Remark 650 | HELIX THERE IS A SINGLE RIGHT-HANDED ALPHA-HELIX IN EACH OF THE MONOMERS PRESENT IN THE ASYMMETRIC UNIT. | ||||||
Remark 700 | SHEET EACH OF THE MONOMERS IN THE ASYMMETRIC UNIT CONTAINS A SINGLE, FIVE-STRAND ANTIPARALLEL BETA-SHEET. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mol.cif.gz | 52 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mol.ent.gz | 38.5 KB | Display | PDB format |
PDBx/mmJSON format | 1mol.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mo/1mol ftp://data.pdbj.org/pub/pdb/validation_reports/mo/1mol | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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: CIS PROLINE - PRO A 40 / 2: CIS PROLINE - PRO A 90 / 3: CIS PROLINE - PRO B 40 / 4: CIS PROLINE - PRO B 90 |
-Components
#1: Protein | Mass: 11083.628 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dioscoreophyllum cumminsii (serendipity berry) References: UniProt: P02882 #2: Water | ChemComp-HOH / | Sequence details | SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE DIFFERENCE | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.61 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.2 / Method: vapor diffusion | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.6 Å / Num. obs: 19162 / % possible obs: 82.9 % / Observed criterion σ(I): 0 / Num. measured all: 59663 / Rmerge(I) obs: 0.0638 |
-Processing
Software |
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Refinement | Resolution: 1.7→6 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 1.7→6 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 17089 / Rfactor all: 0.188 / Rfactor obs: 0.174 / Rfactor Rwork: 0.174 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 23.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 2.86 |