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- PDB-2mad: THE ACTIVE SITE STRUCTURE OF METHYLAMINE DEHYDROGENASE: HYDRAZINE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2mad | |||||||||
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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 / 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 Thiobacillius 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 | ![]() | 52.5 KB | Display | ![]() |
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PDB format | ![]() | 34.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 372.2 KB | Display | ![]() |
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Full document | ![]() | 378.4 KB | Display | |
Data in XML | ![]() | 5.3 KB | Display | |
Data in CIF | ![]() | 11.1 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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Atom site foot note | 1: THE QUINONE CONTAINING TRYPTOPHAN (L 57).THE QUINONE OXYGEN IS GIVEN IN HETATM QTR. 2: LYS L 129 - ALA L 130 OMEGA ANGLE = 0.904 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION | ||||||||
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: 13668.154 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: 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 | SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.9 Å3/Da / Density % sol: 74.92 % | |||||||||||||||||||||||||
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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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Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.209 / Highest resolution: 2.25 Å | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.25 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.25 Å / Rfactor obs: 0.209 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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