+Open data
-Basic information
Entry | Database: PDB / ID: 1b5e | ||||||
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Title | DCMP HYDROXYMETHYLASE FROM T4 | ||||||
Components | PROTEIN (DEOXYCYTIDYLATE HYDROXYMETHYLASE) | ||||||
Keywords | TRANSFERASE / HYDROXYMETHYLASE / DNTP SYNTHESIZING COMPLEX | ||||||
Function / homology | Function and homology information deoxycytidylate 5-hydroxymethyltransferase / deoxycytidylate 5-hydroxymethyltransferase activity Similarity search - Function | ||||||
Biological species | Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.6 Å | ||||||
Authors | Song, H.K. / Sohn, S.H. / Suh, S.W. | ||||||
Citation | Journal: EMBO J. / Year: 1999 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b5e.cif.gz | 111 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b5e.ent.gz | 86.2 KB | Display | PDB format |
PDBx/mmJSON format | 1b5e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b5e_validation.pdf.gz | 1023.2 KB | Display | wwPDB validaton report |
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Full document | 1b5e_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1b5e_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 1b5e_validation.cif.gz | 28.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b5/1b5e ftp://data.pdbj.org/pub/pdb/validation_reports/b5/1b5e | HTTPS FTP |
-Related structure data
-Links
-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: (0.630999, 0.000917, 0.775783), Vector: |
-Components
#1: Protein | Mass: 28523.229 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato References: UniProt: P08773, deoxycytidylate 5-hydroxymethyltransferase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 54 % Description: DATA WERE COLLECTED USING THE WEISSENBERG METHOD. | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: pH 8.0 | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
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: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Apr 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 80033 / % possible obs: 97.3 % / Redundancy: 6.4 % / Rsym value: 0.066 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.6→8 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.6→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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |