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Yorodumi- PDB-1mli: CRYSTAL STRUCTURE OF MUCONOLACTONE ISOMERASE AT 3.3 ANGSTROMS RES... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mli | ||||||
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Title | CRYSTAL STRUCTURE OF MUCONOLACTONE ISOMERASE AT 3.3 ANGSTROMS RESOLUTION | ||||||
Components | MUCONOLACTONE ISOMERASE | ||||||
Keywords | INTRAMOLECULAR OXIDOREDUCTASE | ||||||
Function / homology | muconolactone Delta-isomerase / muconolactone delta-isomerase activity / Muconolactone delta-isomerase / Muconolactone isomerase domain / Muconolactone delta-isomerase / beta-ketoadipate pathway / Dimeric alpha-beta barrel / Muconolactone Delta-isomerase Function and homology information | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 3.3 Å | ||||||
Authors | Katti, S.K. / Katz, B.A. / Wyckoff, H.W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1989 Title: Crystal structure of muconolactone isomerase at 3.3 A resolution. Authors: Katti, S.K. / Katz, B.A. / Wyckoff, H.W. #1: Journal: J.Mol.Biol. / Year: 1985 Title: Low Resolution Crystal Structure of Muconolactone Isomerase. A Decamer with a 5-Fold Symmetry Axis Authors: Katz, B.A. / Ollis, D. / Wyckoff, H.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mli.cif.gz | 35.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mli.ent.gz | 21.1 KB | Display | PDB format |
PDBx/mmJSON format | 1mli.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mli_validation.pdf.gz | 294.7 KB | Display | wwPDB validaton report |
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Full document | 1mli_full_validation.pdf.gz | 294.6 KB | Display | |
Data in XML | 1mli_validation.xml.gz | 729 B | Display | |
Data in CIF | 1mli_validation.cif.gz | 8.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/1mli ftp://data.pdbj.org/pub/pdb/validation_reports/ml/1mli | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | MUCONOLACTONE ISOMERASE IS A DECAMER WITH A CLOSED 52 POINT NONCRYSTALLOGRAPHIC SYMMETRY. THE FIVE-FOLD AXIS IS ALMOST ALONG THE A-AXIS. THE TWO-FOLD AXES ARE IN A PLANE PERPENDICULAR TO THE FIVE-FOLD DIRECTION. THE MOLECULAR CENTER IS AT (16.250, 0.692, 19.308). THE TWO-FOLD SYMMETRY OPERATOR IS PRESENTED ON *MTRIX 1* RECORDS BELOW AND THE FIVE-FOLD SYMMETRY OPERATOR IS PRESENTED ON *MTRIX 2* RECORDS BELOW. THE FOLLOWING PROCEDURE CAN BE USED TO GENERATE COORDINATES OF A DECAMER FROM THE MONOMER COORDINATES PRESENTED IN THIS ENTRY. 1. APPLY THE TRANSFORMATION PRESENTED ON THE *MTRIX 1* RECORDS BELOW TO THE MONOMER IN THIS ENTRY TO GENERATE A TWO-FOLD RELATED MONOMER. 2. APPLY THE TRANSFORMATION PRESENTED ON THE *MTRIX 2* RECORDS BELOW TO THE DIMER GENERATED IN STEP 1 TO GENERATE A FIVE-FOLD RELATED DIMER. 3. PERFORM STEP 2 THREE MORE TIMES, EACH TIME APPLYING THE TRANSFORMATION TO THE NEWLY-GENERATED DIMER. THIS WILL YIELD A TOTAL OF FIVE DIMERS (TEN MONOMERS). |
-Components
#1: Protein | Mass: 11175.833 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / References: UniProt: P00948, muconolactone Delta-isomerase |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.77 % | ||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6 / 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: 3.3 Å / Num. obs: 14090 / Rmerge(I) obs: 0.082 |
-Processing
Refinement | Highest resolution: 3.3 Å | ||||||||||||
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Refinement step | Cycle: LAST / Highest resolution: 3.3 Å
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Refinement | *PLUS Num. reflection all: 9329 / Num. reflection obs: 14027 / Rfactor obs: 0.39 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |