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Yorodumi- PDB-5dmn: Crystal Structure of the Homocysteine Methyltransferase MmuM from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dmn | |||||||||
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Title | Crystal Structure of the Homocysteine Methyltransferase MmuM from Escherichia coli, Apo form | |||||||||
Components | Homocysteine S-methyltransferase | |||||||||
Keywords | TRANSFERASE / Homocysteine Methyltransferase | |||||||||
Function / homology | Function and homology information homocysteine S-methyltransferase / S-adenosylmethionine-homocysteine S-methyltransferase activity / S-methylmethionine metabolic process / S-methylmethionine cycle / S-methylmethionine-homocysteine S-methyltransferase activity / methionine biosynthetic process / methylation / DNA damage response / zinc ion binding Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.892 Å | |||||||||
Authors | Li, K. / Li, G. / Bradbury, L.M.T. / Andrew, H.D. / Bruner, S.D. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Biochem.J. / Year: 2016 Title: Crystal structure of the homocysteine methyltransferase MmuM from Escherichia coli. Authors: Li, K. / Li, G. / Bradbury, L.M. / Hanson, A.D. / Bruner, S.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dmn.cif.gz | 109.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dmn.ent.gz | 83.8 KB | Display | PDB format |
PDBx/mmJSON format | 5dmn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dmn_validation.pdf.gz | 451.2 KB | Display | wwPDB validaton report |
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Full document | 5dmn_full_validation.pdf.gz | 455.1 KB | Display | |
Data in XML | 5dmn_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 5dmn_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/5dmn ftp://data.pdbj.org/pub/pdb/validation_reports/dm/5dmn | HTTPS FTP |
-Related structure data
Related structure data | 5dmlC 5dmmC 1q7mS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33457.754 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: mmuM, yagD, b0261, JW0253 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) References: UniProt: Q47690, homocysteine S-methyltransferase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.56 % / Description: rod-shape |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 1.6 M ammonium sulfate, 10% v/v glycerol and 0.1 M sodium acetate, pH 4.8 PH range: 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 22, 2015 |
Radiation | Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.892→38.425 Å / Num. obs: 13530 / % possible obs: 99.71 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.151 / Rsym value: 0.165 / Net I/σ(I): 11.93 |
Reflection shell | Resolution: 2.892→2.99 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 3.54 / % possible all: 98.41 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Q7M Resolution: 2.892→38.425 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.16 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.892→38.425 Å
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Refine LS restraints |
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LS refinement shell |
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