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Yorodumi- PDB-6p8c: 2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate redu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6p8c | ||||||
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Title | 2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate reductase (MthRED) from Methanothermobacter thermautotrophicus | ||||||
Components | 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase | ||||||
Keywords | OXIDOREDUCTASE / Riboflavin / Cofactor / Methanothermobacter thermautotrophicus. | ||||||
Function / homology | Function and homology information 2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate reductase / 5-amino-6-(5-phosphoribosylamino)uracil reductase activity / riboflavin biosynthetic process / NADP binding Similarity search - Function | ||||||
Biological species | Methanothermobacter thermautotrophicus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.07 Å | ||||||
Authors | Carbone, V. / Schofield, L.R. / Hannus, I. / Sutherland-Smith, A.J. / Ronimus, R.S. | ||||||
Funding support | New Zealand, 1items
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Citation | Journal: To Be Published Title: The Crystal Structure of 2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate reductase (MthRED) from Methanothermobacter thermautotrophicus Authors: Carbone, V. / Schofield, L.R. / Hannus, I. / Sutherland-Smith, A.J. / Ronimus, R.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6p8c.cif.gz | 110.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6p8c.ent.gz | 82 KB | Display | PDB format |
PDBx/mmJSON format | 6p8c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6p8c_validation.pdf.gz | 1018.7 KB | Display | wwPDB validaton report |
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Full document | 6p8c_full_validation.pdf.gz | 1023.3 KB | Display | |
Data in XML | 6p8c_validation.xml.gz | 21.9 KB | Display | |
Data in CIF | 6p8c_validation.cif.gz | 30.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p8/6p8c ftp://data.pdbj.org/pub/pdb/validation_reports/p8/6p8c | HTTPS FTP |
-Related structure data
Related structure data | 2aznS S: Starting model for refinement |
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Similar 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:
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 27397.387 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H) (archaea) Strain: ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H Gene: MTH_235 / Production host: Escherichia coli (E. coli) References: UniProt: O26337, 2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate reductase |
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-Non-polymers , 5 types, 275 molecules
#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-MG / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.39 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: 0.2 M magnesium chloride, 10% (w/v) PEG 8000, 0.1 M Na-Cacodylate pH 6.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9184 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 25, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.07→68.698 Å / Num. all: 34024 / Num. obs: 34024 / % possible obs: 99.8 % / Redundancy: 5.3 % / Rpim(I) all: 0.049 / Rrim(I) all: 0.112 / Rsym value: 0.1 / Net I/av σ(I): 5.4 / Net I/σ(I): 10.1 / Num. measured all: 179331 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2AZN Resolution: 2.07→45.981 Å / SU R Cruickshank DPI: 0.1685 / Cross valid method: THROUGHOUT / Details: UTILIZED TLS REFINEMENT FOR FINAL CYCLE
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Displacement parameters | Biso max: 92.41 Å2 / Biso mean: 38.9059 Å2 / Biso min: 18.65 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.07→45.981 Å
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