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Yorodumi- PDB-3ibw: Crystal Structure of the ACT domain from GTP pyrophosphokinase of... -
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-Basic information
Entry | Database: PDB / ID: 3ibw | ||||||
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Title | Crystal Structure of the ACT domain from GTP pyrophosphokinase of Chlorobium tepidum. Northeast Structural Genomics Consortium Target CtR148A | ||||||
Components | GTP pyrophosphokinase | ||||||
Keywords | TRANSFERASE / GTP pyrophosphokinase / ACT domain / kinase / NESG / CtR148A / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
Function / homology | Function and homology information guanosine tetraphosphate metabolic process / GTP diphosphokinase activity / GTP diphosphokinase / RNA binding Similarity search - Function | ||||||
Biological species | Chlorobaculum tepidum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.93 Å | ||||||
Authors | Vorobiev, S. / Su, M. / Seetharaman, J. / Janjua, J. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. ...Vorobiev, S. / Su, M. / Seetharaman, J. / Janjua, J. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the ACT domain from GTP pyrophosphokinase of Chlorobium tepidum. Authors: Vorobiev, S. / Su, M. / Seetharaman, J. / Janjua, J. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ibw.cif.gz | 42.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ibw.ent.gz | 32.7 KB | Display | PDB format |
PDBx/mmJSON format | 3ibw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ib/3ibw ftp://data.pdbj.org/pub/pdb/validation_reports/ib/3ibw | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | dimer according to aggregation screening |
-Components
#1: Protein | Mass: 10238.252 Da / Num. of mol.: 2 / Fragment: ACT domain / Mutation: I667N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlorobaculum tepidum (bacteria) / Strain: ATCC 49652/DSM 12025/TLS / Gene: CT1545, relA / Plasmid: pET 21-23C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q8KC80, GTP diphosphokinase #2: 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: 2.37 Å3/Da / Density % sol: 48.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% PEG 8000, 0.17 ammonium phosphate, 0.085M cacodylic acid, 15% glycerol, pH 6.5 , VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97853 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 10, 2009 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→50 Å / Num. all: 28314 / Num. obs: 28229 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Biso Wilson estimate: 9.5 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 34.9 |
Reflection shell | Resolution: 1.93→1.96 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 9.5 / Num. unique all: 1410 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.93→40.93 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 89532.648 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.35 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.93→40.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.93→2.05 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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