+Open data
-Basic information
Entry | Database: PDB / ID: 1nv9 | ||||||
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Title | HemK, apo structure | ||||||
Components | hemK protein | ||||||
Keywords | TRANSFERASE / Class I methyltransferase fold | ||||||
Function / homology | Function and homology information peptide chain release factor N5-glutamine methyltransferase / protein-(glutamine-N5) methyltransferase activity / protein-glutamine N-methyltransferase activity / methylation / nucleic acid binding Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.356 Å | ||||||
Authors | Schubert, H.L. / Phillips, J.D. / Hill, C.P. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Structures along the Catalytic Pathway of PrmC/HemK, an N(5)-Glutamine AdoMet-Dependent Methyltransferase Authors: Schubert, H.L. / Phillips, J.D. / Hill, C.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nv9.cif.gz | 66.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nv9.ent.gz | 48.4 KB | Display | PDB format |
PDBx/mmJSON format | 1nv9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nv9_validation.pdf.gz | 716.8 KB | Display | wwPDB validaton report |
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Full document | 1nv9_full_validation.pdf.gz | 727.8 KB | Display | |
Data in XML | 1nv9_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 1nv9_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nv/1nv9 ftp://data.pdbj.org/pub/pdb/validation_reports/nv/1nv9 | HTTPS FTP |
-Related structure data
Related structure data | 1nv8SC S: Starting model for refinement C: citing same article (ref.) |
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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: 31781.535 Da / Num. of mol.: 1 / Fragment: HemK Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: HemK / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codon+ References: UniProt: Q9WYV8, Transferases; Transferring one-carbon groups; Methyltransferases |
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#2: Chemical | ChemComp-SAH / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.91 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG3000, Citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 19K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 30, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. all: 13364 / Num. obs: 13340 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.039 / Net I/σ(I): 20 |
Reflection shell | Resolution: 2.35→2.43 Å / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 2.3 / % possible all: 79.4 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 24661 / Num. measured all: 100547 |
Reflection shell | *PLUS % possible obs: 79.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: PDB ENTRY 1NV8 Resolution: 2.356→50 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.892 / SU B: 13.479 / SU ML: 0.326 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.41 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.043 Å2
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Refinement step | Cycle: LAST / Resolution: 2.356→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.356→2.417 Å / Total num. of bins used: 20 /
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Software | *PLUS Version: 5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.35 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.3 / Rfactor Rwork: 0.238 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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