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Yorodumi- PDB-1h7a: Structural basis for allosteric substrate specificity regulation ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h7a | |||||||||
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Title | Structural basis for allosteric substrate specificity regulation in class III ribonucleotide reductases: NRDD in complex with dATP | |||||||||
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: 2.75 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h7a.cif.gz | 127.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h7a.ent.gz | 97.1 KB | Display | PDB format |
PDBx/mmJSON format | 1h7a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1h7a_validation.pdf.gz | 820.5 KB | Display | wwPDB validaton report |
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Full document | 1h7a_full_validation.pdf.gz | 843.9 KB | Display | |
Data in XML | 1h7a_validation.xml.gz | 24.8 KB | Display | |
Data in CIF | 1h7a_validation.cif.gz | 34 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h7/1h7a ftp://data.pdbj.org/pub/pdb/validation_reports/h7/1h7a | HTTPS FTP |
-Related structure data
Related structure data | 1h78C 1h79C 1h7bC 1b8b 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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-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) |
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#2: Chemical | ChemComp-DTP / |
#3: Chemical | ChemComp-FE2 / |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.34 Å3/Da / Density % sol: 71.65 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: 30% PEG 400, 0.2M MGCL2, 0.1M HEPES PH 7.5, 5MM DTT | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Logan, D.T., (1999) Science, 283, 1499. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.0714 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 15, 1998 / Details: BENT MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0714 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→40 Å / Num. obs: 29688 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 61.1 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.75→2.81 Å / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 1 / % possible all: 70 |
Reflection | *PLUS Lowest resolution: 30 Å / % possible obs: 92 % / Rmerge(I) obs: 0.09 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1B8B.PDB 1b8b Resolution: 2.75→29.87 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2332481.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Stereochemistry target values: MAXIMUM LIKELIHOOD FUNCTION ON F Details: THE REGIONS BETWEEN RESIDUES 590 AND 605 ARE NOT SEEN IN THE ELECTRON DENSITY
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.2851 Å2 / ksol: 0.318931 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.75→29.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.92 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 30 Å / Rfactor obs: 0.216 / Rfactor Rfree: 0.259 / Rfactor Rwork: 0.216 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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