+Open data
-Basic information
Entry | Database: PDB / ID: 4lec | ||||||
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Title | Human Methyltransferase-Like Protein 21A | ||||||
Components | Protein-lysine methyltransferase METTL21A | ||||||
Keywords | TRANSFERASE / METTL21A / Methyltransferase / Methyltransferase-Like Protein 21A / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information peptidyl-lysine methylation / protein methyltransferase activity / protein methylation / protein-lysine N-methyltransferase activity / Protein methylation / heat shock protein binding / Hsp70 protein binding / Transferases; Transferring one-carbon groups; Methyltransferases / ATPase binding / protein-containing complex ...peptidyl-lysine methylation / protein methyltransferase activity / protein methylation / protein-lysine N-methyltransferase activity / Protein methylation / heat shock protein binding / Hsp70 protein binding / Transferases; Transferring one-carbon groups; Methyltransferases / ATPase binding / protein-containing complex / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.28 Å | ||||||
Authors | Dong, A. / Zeng, H. / Fenner, M. / Wernimont, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Wu, H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: The Crystal Structure of Human Methyltransferase-Like Protein 21A in Complex with SAH Authors: Zeng, H. / Dong, A. / Wu, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lec.cif.gz | 96.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lec.ent.gz | 72.3 KB | Display | PDB format |
PDBx/mmJSON format | 4lec.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lec_validation.pdf.gz | 948.4 KB | Display | wwPDB validaton report |
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Full document | 4lec_full_validation.pdf.gz | 949.4 KB | Display | |
Data in XML | 4lec_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 4lec_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/le/4lec ftp://data.pdbj.org/pub/pdb/validation_reports/le/4lec | HTTPS FTP |
-Related structure data
Related structure data | 2bzbS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Details | AUTHORS STATE THAT THE BIOLOGICAL MOLECULE IS UNKNOWN. |
-Components
#1: Protein | Mass: 23883.275 Da / Num. of mol.: 2 / Fragment: UNP residues 8-218 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: METTL21A, FAM119A, HCA557B / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pRARE-V2R References: UniProt: Q8WXB1, Transferases; Transferring one-carbon groups; Methyltransferases #2: Chemical | #3: Chemical | ChemComp-UNX / #4: 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: 3.24 Å3/Da / Density % sol: 62.04 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 15% PEG 3350, 0.1 M Succinate Acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: May 31, 2013 / Details: VeriMax HR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→50 Å / Num. all: 27200 / Num. obs: 27200 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 45.17 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 2.28→2.32 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.938 / Mean I/σ(I) obs: 2 / Num. unique all: 1336 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2BZB Resolution: 2.28→36.08 Å / Cor.coef. Fo:Fc: 0.8993 / Cor.coef. Fo:Fc free: 0.8766 / Occupancy max: 1 / Occupancy min: 0.2 / SU R Cruickshank DPI: 0.247 / Cross valid method: THROUGHOUT / σ(F): 0 Details: RAMACHANDRAN OUTLIERS AT ACTIVE SITE, A147 TYR, B147 TYR
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Displacement parameters | Biso max: 97.75 Å2 / Biso mean: 39.068 Å2 / Biso min: 5.92 Å2
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Refine analyze | Luzzati coordinate error obs: 0.331 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.28→36.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.28→2.37 Å / Total num. of bins used: 14
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