+Open data
-Basic information
Entry | Database: PDB / ID: 1rxs | ||||||
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Title | E. coli uridine phosphorylase: 2'-deoxyuridine phosphate complex | ||||||
Components | Uridine phosphorylase | ||||||
Keywords | TRANSFERASE / pentosyltransferase / uridine phosphorylase / 2'-deoxyuridine / induced fit / specificity / potassium | ||||||
Function / homology | Function and homology information uridine catabolic process / uridine phosphorylase / nucleotide catabolic process / uridine phosphorylase activity / UMP salvage / potassium ion binding / DNA damage response / protein-containing complex / ATP binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Caradoc-Davies, T.T. / Cutfield, S.M. / Lamont, I.L. / Cutfield, J.F. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Crystal structures of escherichia coli uridine phosphorylase in two native and three complexed forms reveal basis of substrate specificity, induced conformational changes and influence of potassium Authors: Caradoc-Davies, T.T. / Cutfield, S.M. / Lamont, I.L. / Cutfield, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rxs.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1rxs.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 1rxs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rxs_validation.pdf.gz | 623.8 KB | Display | wwPDB validaton report |
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Full document | 1rxs_full_validation.pdf.gz | 738.5 KB | Display | |
Data in XML | 1rxs_validation.xml.gz | 150.9 KB | Display | |
Data in CIF | 1rxs_validation.cif.gz | 221 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rx/1rxs ftp://data.pdbj.org/pub/pdb/validation_reports/rx/1rxs | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 1 / Label seq-ID: 4 - 253
NCS ensembles :
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-Components
-Protein , 1 types, 30 molecules AaBbCcDdEeFRGPHhIiJjKkLlMmNQOo
#1: Protein | Mass: 27189.055 Da / Num. of mol.: 30 Source method: isolated from a genetically manipulated source Details: This structure consists of thirty monomers, twelve of which are in the closed conformation, thirteen are in the intermediate (partially closed) conformation and five in the open conformation. ...Details: This structure consists of thirty monomers, twelve of which are in the closed conformation, thirteen are in the intermediate (partially closed) conformation and five in the open conformation. The closed and intermediate monomers contain substrate (2'-deoxyuridine and phosphate). Due to the large size of the model it was refined using three template models, each of which was the best observed example of an individual conformation, and shell scripts were written to create the 30 monomer model from these input models and the ncs operators relating them. The vanadate component of this structure is an artifact of the crystal conditions with no functional significance. See "REMARK 3" for further details. Source: (gene. exp.) Escherichia coli (E. coli) / Gene: UDP / Plasmid: pPROEX::pvdS / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P12758, uridine phosphorylase |
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-Non-polymers , 5 types, 1666 molecules
#2: Chemical | ChemComp-K / #3: Chemical | ChemComp-V7O / #4: Chemical | ChemComp-PO4 / #5: Chemical | ChemComp-DUR / #6: Water | ChemComp-HOH / | |
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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: 2.25 Å3/Da / Density % sol: 44.85 % |
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Crystal grow | Temperature: 289 K / Method: batch method under oil / pH: 7.5 Details: TRIS HCL, PEG4000, POTASSIUM ACETATE, 2'-DEOXYURIDINE, SODIUM ORTHOVANADATE, pH 7.50, BATCH METHOD UNDER OIL, temperature 289K |
-Data collection
Diffraction | Mean temperature: 115 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 5, 2002 / Details: OSMIC |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→40.49 Å / Num. all: 173525 / Num. obs: 173525 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 46.18 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 2.8→2.94 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 1.8 / Num. unique all: 19170 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: DETWINNED HEXAMERIC NATIVE UP Resolution: 2.8→26.75 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.905 / SU B: 13.538 / SU ML: 0.262 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC (TLS REFINEMENT) / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: TLS and restrained refinement was carried out using REFMAC5. Each conformation was restrained together using ncs restraints (tight positional (0.05a) and loose thermal (5.0a3) restraints). ...Details: TLS and restrained refinement was carried out using REFMAC5. Each conformation was restrained together using ncs restraints (tight positional (0.05a) and loose thermal (5.0a3) restraints). Each monomer was split into two TLS domains, comprising the mobile and fixed regions of each monomer. This structure consists of thirty monomers, twelve of which are in the closed conformation, thirteen are in the intermediate (partially closed) conformation and five in the open conformation. Closed and intermediate conformation monomers contain substrate (2'-deoxyuridine and phosphate). Due to the large size of the model it was refined using three template models, each of which was the best observed example of an individual conformation, and shell scripts were written to create the 30 monomer model from these input models and the NCS operators relating them. The 30 monomer model was then refined using refmac5 and ncs restraints were applied as a tight positional (0.05a) and loose thermal (5.0a3) restraints. These restraints, along with tls restraints where the mobile and fixed regions of each monomer were treated as separate TLS domains, were applied to each conformation with each member of a conformation being restrained against the template model. The closed conformation monomers have 2000 added to each residue number, the intermediate monomers have 1000 added to each residue number and the open monomers have 3000 added to each reside number. Such renumbering was required for manipulation of the model and to allow the use of ncs restraints in refinement using refmac5. Each monomer has its associated water molecules added to the chain with a residue number starting at 300. Therefore a closed monomer has its first water molecule as residue 2301, an intermediate monomer has 1301 and an open monomer 3301. Residues 254 to 299 are not present in each chain. The twelve closed monomers are in chains: A, B, C, E, G, H, I, J, K, L, M, and P. The thirteen intermediate monomers are in chains B, C, D, E, F, H, I, J, K, N, O, Q, and R. The five open monomers are in chains: A, D, L, M, and O. Lower and upper case chain letters in the released model are equivalent. A large torus of electron density inside the central pore of each hexamer was modelled as a meta-vanavdate ion. Sodium orthovanadate was present in the crystallisation conditions, and therefore the trimeric head of the meta- vanadate ion from 1DKT (Human cyclin dependent kinase subunit type-A complex with meta vanadate) was used as a template model. The vanadate component of this structure is an artifact of the crystal conditions with no functional significance, as two other up substrate complexes have been solved in the absence of vanadate and no density corresponding to metavanadate is observed
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.286 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→26.75 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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