+Open data
-Basic information
Entry | Database: PDB / ID: 3muc | ||||||
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Title | MUCONATE CYCLOISOMERASE VARIANT I54V | ||||||
Components | PROTEIN (MUCONATE CYCLOISOMERASE) | ||||||
Keywords | ISOMERASE / MUCONATE CYCLOISOMERASE / SUBSTRATE SPECIFICITY | ||||||
Function / homology | Function and homology information muconate cycloisomerase / chloromuconate cycloisomerase activity / muconate cycloisomerase activity / beta-ketoadipate pathway / amino acid catabolic process / manganese ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 2.3 Å | ||||||
Authors | Schell, U. / Helin, S. / Kajander, T. / Schlomann, M. / Goldman, A. | ||||||
Citation | Journal: Proteins / Year: 1999 Title: Structural basis for the activity of two muconate cycloisomerase variants toward substituted muconates. Authors: Schell, U. / Helin, S. / Kajander, T. / Schlomann, M. / Goldman, A. #1: Journal: J.Mol.Biol. / Year: 1995 Title: The Refined X-Ray Structure of Muconate Lactonizing Enzyme from Pseudomonas Putida Prs2000 at 1.85 A Resolution Authors: Helin, S. / Kahn, P.C. / Guha, B.L. / Mallows, D.G. / Goldman, A. #2: Journal: Acta Crystallogr.,Sect.D / Year: 1994 Title: Crystal Structure of Chloromuconate Cycloisomerase from Alcaligenes Eutrophus Jmp134 (Pjp4) at 3 A Resolution Authors: Hoier, H. / Schloemann, M. / Hammer, A. / Glusker, J.P. / Carrell, H.L. / Goldman, A. / Stezowski, J.J. / Heinemann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3muc.cif.gz | 150.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3muc.ent.gz | 117.8 KB | Display | PDB format |
PDBx/mmJSON format | 3muc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3muc_validation.pdf.gz | 434.9 KB | Display | wwPDB validaton report |
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Full document | 3muc_full_validation.pdf.gz | 441.2 KB | Display | |
Data in XML | 3muc_validation.xml.gz | 28.6 KB | Display | |
Data in CIF | 3muc_validation.cif.gz | 40.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mu/3muc ftp://data.pdbj.org/pub/pdb/validation_reports/mu/3muc | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.754163, 0.656679, 0.003275), Vector: |
-Components
#1: Protein | Mass: 39864.570 Da / Num. of mol.: 2 / Mutation: I54V / Source method: isolated from a natural source / Source: (natural) Pseudomonas putida (bacteria) / Strain: PRS2000 / References: UniProt: P08310, muconate cycloisomerase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: double dialysis | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 132958 / % possible obs: 80.2 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 9.3 Å2 / Rmerge(I) obs: 0.121 |
Reflection | *PLUS Lowest resolution: 8 Å / Num. obs: 30586 / Num. measured all: 132958 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 2.3→8 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 17.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→8 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS σ(F): 2 / % reflection Rfree: 5.1 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 17.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.271 / % reflection Rfree: 4.6 % / Rfactor Rwork: 0.211 |