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Yorodumi- PDB-1cbk: 7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN-PYROPHOSPHOKINASE FROM HAEMOPHI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cbk | ||||||
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Title | 7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN-PYROPHOSPHOKINASE FROM HAEMOPHILUS INFLUENZAE | ||||||
Components | PROTEIN (7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN-PYROPHOSPHOKINASE) | ||||||
Keywords | TRANSFERASE / PYROPHOSPHOKINASE | ||||||
Function / homology | Function and homology information 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / kinase activity / ATP binding Similarity search - Function | ||||||
Biological species | Haemophilus influenzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.02 Å | ||||||
Authors | Hennig, M. / D'Arcy, A. / Dale, G. / Oefner, C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: The structure and function of the 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase from Haemophilus influenzae. Authors: Hennig, M. / Dale, G.E. / D'arcy, A. / Danel, F. / Fischer, S. / Gray, C.P. / Jolidon, S. / Muller, F. / Page, M.G. / Pattison, P. / Oefner, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cbk.cif.gz | 85 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cbk.ent.gz | 64.5 KB | Display | PDB format |
PDBx/mmJSON format | 1cbk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/1cbk ftp://data.pdbj.org/pub/pdb/validation_reports/cb/1cbk | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | THE ASYMMETRIC UNIT OF THE CRYSTAL CONTAINS ONE DIMER. |
-Components
#1: Protein | Mass: 18320.012 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P43777 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | IN THE INHIBITOR THE CH2-OH SIDE-CHAIN IN POSITION 6 IS MOST LIKELY REPLACED BY OXYGEN. | |
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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: 2.71 Å3/Da / Density % sol: 54.64 % |
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Crystal grow | pH: 8 / Details: pH 8.0 |
Crystal grow | *PLUS pH: 8.5 / Method: unknown / Details: seeding |
Components of the solutions | *PLUS Conc.: 2.8 M / Common name: ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 120 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.9686,0.9796,0.9794 | ||||||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.02→20 Å / Num. obs: 25768 / % possible obs: 98.8 % / Redundancy: 3.8 % / Rsym value: 6.21 | ||||||||||||
Reflection shell | Resolution: 2.02→2.2 Å / Rsym value: 16.7 / % possible all: 96.6 | ||||||||||||
Reflection | *PLUS Num. measured all: 90489 / Rmerge(I) obs: 0.0621 | ||||||||||||
Reflection shell | *PLUS % possible obs: 96.6 % / Rmerge(I) obs: 0.167 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.02→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.02→20 Å
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Refine LS restraints |
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