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- PDB-1jqe: Crystal Structure Analysis of Human Histamine Methyltransferase (... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jqe | ||||||
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Title | Crystal Structure Analysis of Human Histamine Methyltransferase (Ile105 Polymorphic Variant) Complexed with AdoHcy and Antimalarial Drug Quinacrine | ||||||
![]() | Histamine N-Methyltransferase | ||||||
![]() | TRANSFERASE / Classic methyltransferase fold / protein-substrate-cofactor complex / polymorphic variant | ||||||
Function / homology | ![]() histamine N-methyltransferase / histamine catabolic process / histamine N-methyltransferase activity / histamine metabolic process / Histidine catabolism / L-histidine catabolic process / Metabolism of ingested SeMet, Sec, MeSec into H2Se / respiratory gaseous exchange by respiratory system / methylation / centrosome ...histamine N-methyltransferase / histamine catabolic process / histamine N-methyltransferase activity / histamine metabolic process / Histidine catabolism / L-histidine catabolic process / Metabolism of ingested SeMet, Sec, MeSec into H2Se / respiratory gaseous exchange by respiratory system / methylation / centrosome / extracellular exosome / nucleoplasm / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Horton, J.R. / Sawada, K. / Nishibori, M. / Zhang, X. / Cheng, X. | ||||||
![]() | ![]() Title: Two polymorphic forms of human histamine methyltransferase: structural, thermal, and kinetic comparisons. Authors: Horton, J.R. / Sawada, K. / Nishibori, M. / Zhang, X. / Cheng, X. #1: ![]() Title: Histamine N-methyltransferase pharmacogenetics: association of a common functional polymorphism with asthma Authors: Yan, L. / Galinsky, R.E. / Bernstein, J.A. / Liggett, S.B. / Weinshilboum, R.M. #2: ![]() Title: Methylation pharmacogenetics: catechol O-methyltransferase, thiopurine methyltransferase, and histamine N-methyltransferase Authors: Weinshilboum, R.M. / Otterness, D.M. / Szumlanski, C.L. #3: ![]() Title: Human histamine N-methyltransferase gene: structural characterization and chromosomal location Authors: Aksoy, S. / Raftogianis, R. / Weinshilboum, R.M. | ||||||
History |
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Remark 600 | HETEROGEN The density for the QUN molecule associated with monomer B is not very good. However, ...HETEROGEN The density for the QUN molecule associated with monomer B is not very good. However, some density in this region was modelled and these atoms were labelled as residue UNX, atom type UNK. Based on the QUN associated with monomer A, atoms UNX 150, 151, 152, and 376 are where the aromatic rings of a QUN could be. Atoms UNX 133 and 134 are where the amide tail of QUN could be. UNX 149 is where the side chain of B Tyr 15 could be. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 131.8 KB | Display | ![]() |
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PDB format | ![]() | 100.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-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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Components
#1: Protein | Mass: 33345.070 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-QUN / | #4: Chemical | ChemComp-UNX / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.9 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: PEG 8000, sodium phosphate, citric acid, sodium chloride, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: May 17, 2000 |
Radiation | Monochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→25 Å / Num. all: 214586 / Num. obs: 202140 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 38.1 |
Reflection shell | Resolution: 1.91→1.94 Å / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 3 / Num. unique all: 1036 / % possible all: 43.8 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. obs: 44743 / Num. measured all: 202140 / Rmerge(I) obs: 0.033 |
Reflection shell | *PLUS % possible obs: 43.8 % / Num. unique obs: 946 / Num. measured obs: 4447 / Rmerge(I) obs: 0.213 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Partially refined 3.3A SeMet HNMT/AdoMet/Histamine structure solved by MAD phasing (crystal grown at pH 7.5). Resolution: 1.91→25 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Residues listed in remark 470 had little or no side chain density. Many residues at N-terminus had no or little visible density for protein backbone. The density for the ligand QUN ...Details: Residues listed in remark 470 had little or no side chain density. Many residues at N-terminus had no or little visible density for protein backbone. The density for the ligand QUN associated with chain B is not very good and is not included in the coordinates section. Some densities were modelled as water molecules even though the refined water molecules were greater than 3.5 Angstroms away from macromolecule atoms. These densities were indeed visible as discrete "water oxygen"-like densities but could represent moities other than water.
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Displacement parameters | Biso mean: 34.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.91→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.91→1.94 Å / Rfactor Rfree error: 0.027
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Refinement | *PLUS Lowest resolution: 25 Å / Rfactor all: 0.21 / Rfactor obs: 0.199 / Rfactor Rfree: 0.239 / Rfactor Rwork: 0.195 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.269 / Rfactor Rwork: 0.235 |