+Open data
-Basic information
Entry | Database: PDB / ID: 2dv3 | ||||||
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Title | Crystal structure of Leu65 to Arg mutant of Diphthine synthase | ||||||
Components | diphthine synthase | ||||||
Keywords | TRANSFERASE / structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information diphthine synthase / diphthine synthase activity / protein histidyl modification to diphthamide / methylation Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Mizutani, H. / Matsuura, Y. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of diphthine synthase from Pyrococcus horikoshii OT3 Authors: Mizutani, H. / Matsuura, Y. / Kunishima, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dv3.cif.gz | 127.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dv3.ent.gz | 97.4 KB | Display | PDB format |
PDBx/mmJSON format | 2dv3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dv3_validation.pdf.gz | 803.6 KB | Display | wwPDB validaton report |
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Full document | 2dv3_full_validation.pdf.gz | 809.7 KB | Display | |
Data in XML | 2dv3_validation.xml.gz | 25.9 KB | Display | |
Data in CIF | 2dv3_validation.cif.gz | 37.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dv/2dv3 ftp://data.pdbj.org/pub/pdb/validation_reports/dv/2dv3 | HTTPS FTP |
-Related structure data
Related structure data | 1vceC 2dsgC 2dshC 2dsiC 2dv4C 2dv5C 2dv7C 2dxvC 2dxwC 2dxxC 2e07C 2e08C 2e15C 2e16C 2e17C 2e7rC 2egbC 2eglC 2egsC 2ehcC 2ehlC 2z6rC 1wngS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 29657.404 Da / Num. of mol.: 2 / Mutation: L65R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: dphB / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O58456, diphthine synthase |
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-Non-polymers , 6 types, 395 molecules
#2: Chemical | ChemComp-NA / | ||||
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#3: Chemical | ChemComp-SAH / | ||||
#4: Chemical | ChemComp-CL / | ||||
#5: Chemical | #6: Chemical | ChemComp-FMT / | #7: 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: 3.15 Å3/Da / Density % sol: 60.98 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 5.8 Details: 3.85M Na Formate, 0.1M acetate, pH 5.8, microbatch, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: May 19, 2006 |
Radiation | Monochromator: bending magnet / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 60256 / Num. obs: 60256 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.065 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 6.43 / Num. unique all: 5913 / Rsym value: 0.349 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1WNG Resolution: 1.9→30 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2480876.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 59.4888 Å2 / ksol: 0.379409 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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