+Open data
-Basic information
Entry | Database: PDB / ID: 4y4n | ||||||
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Title | Thiazole synthase Thi4 from Methanococcus igneus | ||||||
Components | Putative ribose 1,5-bisphosphate isomerase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / thiazole synthase / ISOMERASE | ||||||
Function / homology | Function and homology information sulfide-dependent adenosine diphosphate thiazole synthase / thiazole biosynthetic process / pentosyltransferase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / iron ion binding Similarity search - Function | ||||||
Biological species | Methanotorris igneus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Zhang, X. / Ealick, S.E. | ||||||
Citation | Journal: Biochemistry / Year: 2016 Title: Structural Basis for Iron-Mediated Sulfur Transfer in Archael and Yeast Thiazole Synthases. Authors: Zhang, X. / Eser, B.E. / Chanani, P.K. / Begley, T.P. / Ealick, S.E. #1: Journal: To Be Published Title: Sulfur Transfer Strategies in Thiamin Thiazole Biosynthesis: New Insights from Methanococcus Jannaschii Thi4 Authors: Eser, B. / Zhang, X. / Ealick, S.E. / Begley, T.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4y4n.cif.gz | 402.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y4n.ent.gz | 328.2 KB | Display | PDB format |
PDBx/mmJSON format | 4y4n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y4/4y4n ftp://data.pdbj.org/pub/pdb/validation_reports/y4/4y4n | HTTPS FTP |
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-Related structure data
Related structure data | 4y4lC 4y4mC 1rp0S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
#1: Protein | Mass: 30843.262 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanotorris igneus (archaea) / Strain: DSM 5666 / JCM 11834 / Kol 5 / Gene: Metig_0735 / Production host: Escherichia coli (E. coli) References: UniProt: F6BCS4, ribose-1,5-bisphosphate isomerase #2: Chemical | ChemComp-FE2 / #3: Chemical | ChemComp-48H / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.86 % |
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Crystal grow | Temperature: 295 K / Method: evaporation / pH: 9.5 Details: 1 M Sodium citrate tribasic 0.1 M CHES/ Sodium hydroxide pH 9.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 7, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 136825 / % possible obs: 98.6 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/av σ(I): 2.3 / Net I/σ(I): 19.7 |
Reflection shell | Redundancy: 3.4 % / Rmerge(I) obs: 0.049 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.049 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RP0 Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.956 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.153 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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