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- PDB-2tmd: CORRELATION OF X-RAY DEDUCED AND EXPERIMENTAL AMINO ACID SEQUENCE... -

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Entry
Database: PDB / ID: 2tmd
TitleCORRELATION OF X-RAY DEDUCED AND EXPERIMENTAL AMINO ACID SEQUENCES OF TRIMETHYLAMINE DEHYDROGENASE
ComponentsTRIMETHYLAMINE DEHYDROGENASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


trimethylamine dehydrogenase / trimethylamine dehydrogenase activity / catabolic process / FMN binding / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Trimethylamine dehydrogenase/Dimethylamine dehydrogenase, FMN-binding domain / : / OYE-like second alpha/beta domain / : / NAD(P)-binding Rossmann-like domain / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain ...Trimethylamine dehydrogenase/Dimethylamine dehydrogenase, FMN-binding domain / : / OYE-like second alpha/beta domain / : / NAD(P)-binding Rossmann-like domain / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Aldolase class I / Aldolase-type TIM barrel / NAD(P)-binding Rossmann-like Domain / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / FLAVIN MONONUCLEOTIDE / IRON/SULFUR CLUSTER / Trimethylamine dehydrogenase
Similarity search - Component
Biological speciesMethylophilus methylotrophus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsMathews, F.S. / Lim, L.W. / White, S.
Citation
Journal: J.Biol.Chem. / Year: 1992
Title: Correlation of x-ray deduced and experimental amino acid sequences of trimethylamine dehydrogenase.
Authors: Barber, M.J. / Neame, P.J. / Lim, L.W. / White, S. / Matthews, F.S.
#1: Journal: J.Biol.Chem. / Year: 1989
Title: Studies of Crystalline Trimethylamine Dehydrogenase in Three Oxidation States and in the Presence of Substrate and Inhibitor
Authors: Bellamy, H.D. / Lim, L.W. / Mathews, F.S. / Dunham, W.R.
#2: Journal: J.Biol.Chem. / Year: 1988
Title: Identification of Adp in the Iron-Sulfur Flavoprotein Trimethylamine Dehydrogenase
Authors: Lim, L.W. / Mathews, F.S. / Steenkamp, D.J.
#3: Journal: J.Biol.Chem. / Year: 1986
Title: Three-Dimensional Structure of the Iron-Sulfur Flavoprotein Trimethylamine Dehydrogenase at 2.4 Angstroms Resolution
Authors: Lim, L.W. / Shamala, N. / Mathews, F.S. / Steenkamp, D.J. / Hamlin, R. / Xuong, N.H.
History
DepositionOct 15, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRIMETHYLAMINE DEHYDROGENASE
B: TRIMETHYLAMINE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,6828
Polymers163,2122
Non-polymers2,4706
Water10,467581
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16140 Å2
ΔGint-95 kcal/mol
Surface area44710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.750, 71.950, 83.820
Angle α, β, γ (deg.)90.00, 97.69, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: THR A 70 - HIS A 71 OMEGA = 17.29 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: THR B 70 - HIS B 71 OMEGA = 16.18 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.971338, 0.217797, 0.095224), (0.210859, 0.604543, 0.768158), (0.109736, 0.766219, -0.63314)
Vector: 66.4754, -15.99959, 14.45649)
DetailsTHERE ARE TWO MOLECULES IN THE ASYMMETRIC UNIT. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*.

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Components

#1: Protein TRIMETHYLAMINE DEHYDROGENASE


Mass: 81606.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylophilus methylotrophus (bacteria)
Strain: W3A1 / References: UniProt: P16099, EC: 1.5.99.7
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 581 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.51 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Details: taken from Lim, L. et al (1982). J. Mol. Biol., 162, 869-876., macro-seeding
Components of the solutions
*PLUS
Conc.: 10-12 % / Common name: PEG8000

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Data collection

Reflection
*PLUS
Highest resolution: 2.4 Å / Num. obs: 133000 / Num. measured all: 430000 / Rmerge(I) obs: 0.032

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.4→10 Å / Rfactor Rwork: 0.154 / Rfactor obs: 0.154
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11482 0 132 581 12195
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.281
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 10 Å / Rfactor obs: 0.154
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.281

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