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Open data
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Basic information
Entry | Database: PDB / ID: 4y4m | ||||||
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Title | Thiazole synthase Thi4 from Methanocaldococcus jannaschii | ||||||
![]() | Putative ribose 1,5-bisphosphate isomerase | ||||||
![]() | BIOSYNTHETIC PROTEIN / Thiazole synthase / ISOMERASE | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, X. / Ealick, S.E. | ||||||
![]() | ![]() 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 393.5 KB | Display | ![]() |
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PDB format | ![]() | 319.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.3 MB | Display | ![]() |
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Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 72.4 KB | Display | |
Data in CIF | ![]() | 93.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4y4lC ![]() 4y4nC ![]() 1rp0S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: 31371.217 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440 Gene: MJ0601 / Production host: ![]() ![]() References: UniProt: Q58018, ribose-1,5-bisphosphate isomerase #2: Chemical | ChemComp-48F / [[( #3: Chemical | ChemComp-NHE / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 60.7 % |
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Crystal grow | Temperature: 295 K / Method: evaporation / pH: 9.5 Details: 1.05 M Potassium/sodium tartrate, 0.1 M CHES/ Sodium hydroxide pH 9.5, 0.2 M Lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 18, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→40 Å / Num. obs: 72800 / % possible obs: 99.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/av σ(I): 2.3 / Net I/σ(I): 13.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1RP0 Resolution: 2.71→40 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.944 / Cross valid method: THROUGHOUT / ESU R: 0.787 / ESU R Free: 0.268 / 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: 54.853 Å2
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Refinement step | Cycle: LAST / Resolution: 2.71→40 Å
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Refine LS restraints |
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