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Yorodumi- PDB-6yb9: Human octameric PAICS in complex with SAICAR, AMP-PNP, and magnesium -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yb9 | ||||||||||||
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Title | Human octameric PAICS in complex with SAICAR, AMP-PNP, and magnesium | ||||||||||||
Components | Multifunctional protein ADE2 | ||||||||||||
Keywords | BIOSYNTHETIC PROTEIN / de novo purine biosynthesis / nucleotide metabolism / cancer target | ||||||||||||
Function / homology | Function and homology information phosphoribosylaminoimidazole carboxylase / : / phosphoribosylaminoimidazole carboxylase activity / phosphoribosylaminoimidazolesuccinocarboxamide synthase / phosphoribosylaminoimidazolesuccinocarboxamide synthase activity / purine nucleobase biosynthetic process / 'de novo' XMP biosynthetic process / Purine ribonucleoside monophosphate biosynthesis / 'de novo' AMP biosynthetic process / GMP biosynthetic process ...phosphoribosylaminoimidazole carboxylase / : / phosphoribosylaminoimidazole carboxylase activity / phosphoribosylaminoimidazolesuccinocarboxamide synthase / phosphoribosylaminoimidazolesuccinocarboxamide synthase activity / purine nucleobase biosynthetic process / 'de novo' XMP biosynthetic process / Purine ribonucleoside monophosphate biosynthesis / 'de novo' AMP biosynthetic process / GMP biosynthetic process / 'de novo' IMP biosynthetic process / cadherin binding / extracellular exosome / ATP binding / identical protein binding / membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.406 Å | ||||||||||||
Authors | Skerlova, J. / Unterlass, J. / Gottmann, M. / Homan, E. / Helleday, T. / Jemth, A.S. / Stenmark, P. | ||||||||||||
Funding support | Sweden, European Union, Czech Republic, 3items
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Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Crystal structures of human PAICS reveal substrate and product binding of an emerging cancer target. Authors: Skerlova, J. / Unterlass, J. / Gottmann, M. / Marttila, P. / Homan, E. / Helleday, T. / Jemth, A.S. / Stenmark, P. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yb9.cif.gz | 188.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yb9.ent.gz | 146.5 KB | Display | PDB format |
PDBx/mmJSON format | 6yb9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yb9_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 6yb9_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6yb9_validation.xml.gz | 34.7 KB | Display | |
Data in CIF | 6yb9_validation.cif.gz | 48.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yb/6yb9 ftp://data.pdbj.org/pub/pdb/validation_reports/yb/6yb9 | HTTPS FTP |
-Related structure data
Related structure data | 6yb8C 2h31S 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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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 7 - 425 / Label seq-ID: 7 - 425
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 47135.102 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PAICS, ADE2, AIRC, PAIS / Production host: Escherichia coli (E. coli) References: UniProt: P22234, phosphoribosylaminoimidazolesuccinocarboxamide synthase, phosphoribosylaminoimidazole carboxylase |
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-Non-polymers , 5 types, 300 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-MG / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.8 Å3/Da / Density % sol: 56.04 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 6 mg/ml PAICS with 5 mM SAICAR, 5 mM AMP-PNP, and 10 mM MgCl2; 0.1 M MES/imidazole pH 6.5, 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M ...Details: 6 mg/ml PAICS with 5 mM SAICAR, 5 mM AMP-PNP, and 10 mM MgCl2; 0.1 M MES/imidazole pH 6.5, 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium L-tartrate, and 0.02 M sodium oxamate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 15, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.406→47.33 Å / Num. obs: 41224 / % possible obs: 99 % / Redundancy: 10.876 % / Biso Wilson estimate: 39.747 Å2 / CC1/2: 0.966 / Rmerge(I) obs: 0.336 / Rrim(I) all: 0.353 / Χ2: 0.987 / Net I/σ(I): 5.16 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2h31 Resolution: 2.406→47.33 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.919 / SU R Cruickshank DPI: 0.3412 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.341 / ESU R Free: 0.237 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 144.47 Å2 / Biso mean: 39.167 Å2 / Biso min: 19.63 Å2
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Refinement step | Cycle: final / Resolution: 2.406→47.33 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 12954 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.406→2.468 Å / Rfactor Rfree error: 0
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