[English] 日本語
Yorodumi- PDB-1h78: STRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE SPECIFICITY REGULATION ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h78 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | STRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE SPECIFICITY REGULATION IN CLASS III RIBONUCLEOTIDE REDUCTASES: NRDD IN COMPLEX WITH DCTP. | |||||||||
Components | ANAEROBIC RIBONUCLEOTIDE-TRIPHOSPHATE REDUCTASE LARGE CHAIN | |||||||||
Keywords | OXIDOREDUCTASE / REDUCTASE / ALLOSTERIC REGULATION / SUBSTRATE SPECIFICITY | |||||||||
Function / homology | Function and homology information 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 | BACTERIOPHAGE T4 (virus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Larsson, K.-M. / Andersson, J. / Sjoeberg, B.-M. / Nordlund, P. / Logan, D.T. | |||||||||
Citation | Journal: Structure / Year: 2001 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1h78.cif.gz | 123.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1h78.ent.gz | 94.1 KB | Display | PDB format |
PDBx/mmJSON format | 1h78.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1h78_validation.pdf.gz | 483.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1h78_full_validation.pdf.gz | 500.4 KB | Display | |
Data in XML | 1h78_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 1h78_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h7/1h78 ftp://data.pdbj.org/pub/pdb/validation_reports/h7/1h78 | HTTPS FTP |
-Related structure data
Related structure data | 1h79C 1h7aC 1h7bC 1b8b C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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.) BACTERIOPHAGE T4 (virus) / Plasmid: PET29T4NRDD(G580A) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109(DE3) References: UniProt: Q9T0V5, UniProt: P07071*PLUS, ribonucleoside-triphosphate reductase (thioredoxin) | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.27 Å3/Da / Density % sol: 71.21 % |
---|---|
Crystal grow | pH: 7.5 / Details: PEG 400, MGCL2, HEPES, DTT, pH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.0266 |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.1816 Å2 / ksol: 0.345733 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.5 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→19.96 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
|