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- PDB-1maf: The Active Site Structure of Methylamine Dehydrogenase: Hydrazine... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1maf | ||||||
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Title | The Active Site Structure of Methylamine Dehydrogenase: Hydrazines Identify C6 as the Reactive Site of the Tryptophan Derived Quinone Cofactor | ||||||
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![]() | OXIDOREDUCTASE(CHNH2(D)-DEAMINATING) | ||||||
Function / homology | ![]() methylamine dehydrogenase (amicyanin) / methylamine dehydrogenase (amicyanin) activity / methylamine metabolic process / aliphatic amine dehydrogenase activity / amine metabolic process / outer membrane-bounded periplasmic space / periplasmic space Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Huizinga, E.G. / Vellieux, F.M.D. / Hol, W.G.J. | ||||||
![]() | ![]() Title: Active site structure of methylamine dehydrogenase: hydrazines identify C6 as the reactive site of the tryptophan-derived quinone cofactor. Authors: Huizinga, E.G. / van Zanten, B.A. / Duine, J.A. / Jongejan, J.A. / Huitema, F. / Wilson, K.S. / Hol, W.G. #1: ![]() Title: Crystallographic Investigations of the Tryptophan-Derived Cofactor in the Quinoprotein Methylamine Dehydrogenase Authors: Chen, L. / Mathews, F.S. / Davidson, V.L. / Huizinga, E.G. / Vellieux, F.M.D. / Duine, J.A. / Hol, W.G.J. #2: ![]() Title: Structure of Quinoprotein Methylamine Dehydrogenase at 2.25 Angstroms Resolution Authors: Vellieux, F.M.D. / Huitema, F. / Groendijk, H. / Kalk, K.H. / Frank, J. / Jongejan, J.A. / Duine, J.A. / Petratos, K. / Drenth, J. / Hol, W.G.J. #3: ![]() Title: Purification, Crystallization and Preliminary X-Ray Investigation of Quinoprotein Methylamine Dehydrogenase from Thiobacillus Versutus Authors: Vellieux, F.M.D. / Frank, J. / Swarte, M.B.A. / Groendijk, H. / Duine, J.A. / Drenth, J. / Hol, W.G.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 53.4 KB | Display | ![]() |
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PDB format | ![]() | 35.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 384.8 KB | Display | ![]() |
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Full document | ![]() | 390.4 KB | Display | |
Data in XML | ![]() | 5 KB | Display | |
Data in CIF | ![]() | 11 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | THE MOLECULE IS NORMALLY A TETRAMER. THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONSISTS OF ONE-HALF OF THE TETRAMER, NAMELY ONE LIGHT CHAIN *L* AND ONE HEAVY CHAIN *H*. TO GENERATE THE FULL MOLECULE, THE FOLLOWING CRYSTALLOGRAPHIC TWO-FOLD OPERATION MUST BE APPLIED TO THE LIGHT AND HEAVY CHAINS PRESENTED IN THIS ENTRY -0.5 0.866025 0.0 0.0 0.866025 0.5 0.0 0.0 0.0 0.0 -1.0 208.368 |
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Components
#1: Protein | Mass: 13654.172 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() |
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#2: Protein | Mass: 38031.996 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() |
#3: Chemical | ChemComp-HDZ / |
#4: Water | ChemComp-HOH / |
Compound details | THE L SUBUNIT CONTAINS THE SIDE CHAIN DERIVED COFACTOR TRYPTOPHYL TRYTOPHAN-QUINONE (MCINTYRE ET AL. ...THE L SUBUNIT CONTAINS THE SIDE CHAIN DERIVED COFACTOR TRYPTOPHYL |
Sequence details | FOR THE H-SUBUNIT THE SEQUENCE GIVEN IN THE SEQRES RECORDS IS AN *X-RAY SEQUENCE*, WHICH WAS ...FOR THE H-SUBUNIT THE SEQUENCE GIVEN IN THE SEQRES RECORDS IS AN *X-RAY SEQUENCE*, WHICH WAS ESTABLISHE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.91 Å3/Da / Density % sol: 74.93 % | |||||||||||||||||||||||||
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Crystal grow | Details: CRYSTALLIZATION OF THE (2,2,2)-TRIFLUOROETHYLHYDRAZINE INHIBITED ENZYME WAS DONE BY THE HANGING DROP METHOD WITH BUFFER 0.1 M NA ACETATE AT PH 5.0. THE PRECIPITANT WAS 42 PER CENT AMMONIUM SULFATE. | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 5 / Method: vapor diffusion, hanging dropDetails: taken from Ubbink, M. et al (1991). Eur. J. Biochem., 202, 1003-1012. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.6 Å / Num. obs: 31580 / % possible obs: 98.4 % / Num. measured all: 66005 / Rmerge(I) obs: 0.051 |
Reflection shell | *PLUS % possible obs: 96.4 % / Rmerge(I) obs: 0.178 |
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Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.188 / Highest resolution: 2.6 Å Details: ALTHOUGH CLEAR EXTRA DENSITY WAS OBSERVED IN THE ACTIVE SITE, THERE WAS NOT SUFFICIENT DENSITY PRESENT TO ACCOMMODATE THE COMPLETE INHIBITOR (FOR DETAILS SEE ARTICLE SPECIFIED ON JRNL CARD). ...Details: ALTHOUGH CLEAR EXTRA DENSITY WAS OBSERVED IN THE ACTIVE SITE, THERE WAS NOT SUFFICIENT DENSITY PRESENT TO ACCOMMODATE THE COMPLETE INHIBITOR (FOR DETAILS SEE ARTICLE SPECIFIED ON JRNL CARD). TWO ATOMS OF THE INHIBITOR, TENTATIVELY IDENTIFIED AS NITROGENS HAVE BEEN INCLUDED IN THE MODEL. | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.6 Å
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Refine LS restraints |
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Refinement | *PLUS | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |