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Yorodumi- PDB-1xje: Structural mechanism of allosteric substrate specificity in a rib... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xje | ||||||
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Title | Structural mechanism of allosteric substrate specificity in a ribonucleotide reductase: dTTP-GDP complex | ||||||
Components | ribonucleotide reductase, B12-dependent | ||||||
Keywords | OXIDOREDUCTASE / ribonucleotide reductase / 10 alpha-beta barrel / protein-nucleotide complex / substrate specificity / allosteric regulation | ||||||
Function / homology | Function and homology information cobalamin binding / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / DNA biosynthetic process / ATP binding Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Larsson, K.-M. / Jordan, A. / Eliasson, R. / Reichard, P. / Logan, D.T. / Nordlund, P. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2004 Title: Structural mechanism of allosteric substrate specificity regulation in a ribonucleotide reductase. Authors: Larsson, K.-M. / Jordan, A. / Eliasson, R. / Reichard, P. / Logan, D.T. / Nordlund, P. | ||||||
History |
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Remark 999 | SEQUENCE Residue 205 is a tyrosine in GB NP_227934 but no density for atoms beyond CB can be found ...SEQUENCE Residue 205 is a tyrosine in GB NP_227934 but no density for atoms beyond CB can be found in an otherwise ordered loop, suggesting sequencing error or spontaneous mutation. The authors suggest a point mutation either in the sequencing clone (SER->TYR mutation) or in their expression clone (TYR->SER). Codons for TYR=ATA and SER=AGA. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xje.cif.gz | 281.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xje.ent.gz | 222.2 KB | Display | PDB format |
PDBx/mmJSON format | 1xje.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xje_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 1xje_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 1xje_validation.xml.gz | 54.5 KB | Display | |
Data in CIF | 1xje_validation.cif.gz | 79.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xj/1xje ftp://data.pdbj.org/pub/pdb/validation_reports/xj/1xje | HTTPS FTP |
-Related structure data
Related structure data | 1xjfC 1xjgC 1xjjC 1xjkC 1xjmC 1xjnC 1r1rS 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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Details | The asymmetric unit consists of a dimer which is the apparent biological unit. |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 73374.234 Da / Num. of mol.: 2 / Fragment: residues 1-644 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: nrdj / Plasmid: pET-22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: O33839, ribonucleoside-diphosphate reductase |
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-Non-polymers , 5 types, 798 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / | #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: 2.63 Å3/Da / Density % sol: 53.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: PEG8000, sodium acetate, sodium chloride, dithiotreithol, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.811 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 23, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.811 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→18 Å / Num. obs: 119507 / % possible obs: 97.2 % / Redundancy: 2.7 % / Rsym value: 0.07 / Net I/σ(I): 12.23 |
Reflection shell | Resolution: 1.9→1.97 Å / Mean I/σ(I) obs: 3.2 / Rsym value: 0.399 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1R1R Resolution: 1.9→18 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.478 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.137 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.972 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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