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- PDB-1h78: STRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE SPECIFICITY REGULATION ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1h78 | |||||||||
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Title | STRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE SPECIFICITY REGULATION IN CLASS III RIBONUCLEOTIDE REDUCTASES: NRDD IN COMPLEX WITH DCTP. | |||||||||
![]() | ANAEROBIC RIBONUCLEOTIDE-TRIPHOSPHATE REDUCTASE LARGE CHAIN | |||||||||
![]() | OXIDOREDUCTASE / REDUCTASE / ALLOSTERIC REGULATION / SUBSTRATE SPECIFICITY | |||||||||
Function / homology | ![]() ribonucleoside-triphosphate reductase (formate) / anaerobic ribonucleoside-triphosphate reductase complex / ribonucleoside-triphosphate reductase (thioredoxin) activity / 2'-deoxyribonucleotide biosynthetic process / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / DNA replication / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Larsson, K.-M. / Andersson, J. / Sjoeberg, B.-M. / Nordlund, P. / Logan, D.T. | |||||||||
![]() | ![]() Title: Structural Basis for Allosteric Substrate Specificty Regulation in Anaerobic Ribonucleotide Reductase Authors: Larsson, K.-M. / Andersson, J. / Sjoeberg, B.-M. / Nordlund, P. / Logan, D.T. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 123.6 KB | Display | ![]() |
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PDB format | ![]() | 94.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1h79C ![]() 1h7aC ![]() 1h7bC ![]() 1b8b 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 68055.594 Da / Num. of mol.: 1 / Fragment: ACTIVE SITE SUBUNIT RESIDUES 1-605 / Mutation: YES Source method: isolated from a genetically manipulated source Details: SEQUENCE DETERMINATION\: YOUNG, P., OHMAN, M., XU, M.Q. Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9T0V5, UniProt: P07071*PLUS, ribonucleoside-triphosphate reductase (thioredoxin) | ||||
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#2: Chemical | #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.27 Å3/Da / Density % sol: 71.21 % |
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Crystal grow | pH: 7.5 / Details: PEG 400, MGCL2, HEPES, DTT, pH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 15, 1999 / Details: BENT MIRROR |
Radiation | Monochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0266 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 41517 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 52.6 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 21 |
Reflection shell | Resolution: 2.5→2.53 Å / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 3.3 / % possible all: 97.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1B8B.PDB ![]() 1b8b Resolution: 2.5→19.96 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: MLF TARGET FUNCTION RESIDUES 544-571 NOT MODELLED BUT HAVE WEAK DENSITY
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.1816 Å2 / ksol: 0.345733 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→19.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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