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Open data
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Basic information
Entry | Database: PDB / ID: 1b5d | ||||||
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Title | DCMP Hydroxymethylase from T4 (Intact) | ||||||
![]() | PROTEIN (DEOXYCYTIDYLATE HYDROXYMETHYLASE) | ||||||
![]() | TRANSFERASE / HYDROXYMETHYLASE / DNTP SYNTHESIZING COMPLEX | ||||||
Function / homology | ![]() deoxycytidylate 5-hydroxymethyltransferase / deoxycytidylate 5-hydroxymethyltransferase activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Song, H.K. / Sohn, S.H. / Suh, S.W. | ||||||
![]() | ![]() Title: Crystal structure of deoxycytidylate hydroxymethylase from bacteriophage T4, a component of the deoxyribonucleoside triphosphate-synthesizing complex. Authors: Song, H.K. / Sohn, S.H. / Suh, S.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 112.4 KB | Display | ![]() |
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PDB format | ![]() | 87.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1022 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 20.7 KB | Display | |
Data in CIF | ![]() | 28.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.628872, -6.0E-6, 0.777509), Vector: |
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Components
#1: Protein | Mass: 28523.229 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: P08773, deoxycytidylate 5-hydroxymethyltransferase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 54 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: pH 8.0 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Song, S.H., (1999) Acta Crystallogr. D55, 1061. / pH: 8.73 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Jun 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 28632 / % possible obs: 90 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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Xplor file | Serial no: 3 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO |