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- PDB-1djq: STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF RECOMBINANT C30A M... -

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Basic information

Entry
Database: PDB / ID: 1djq
TitleSTRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF RECOMBINANT C30A MUTANT OF TRIMETHYLAMINE DEHYDROGENASE FROM METHYLOPHILUS METHYLOTROPHUS (SP. W3A1)
ComponentsTRIMETHYLAMINE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / IRON-SULFUR FLAVOPROTEIN / ELECTRON TRANSFER
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: 2.2 Å
AuthorsTrickey, P. / Basran, J. / Lian, L.-Y. / Chen, Z.-W. / Barton, J.D. / Sutcliffe, M.J. / Scrutton, N.S. / Mathews, F.S.
Citation
Journal: Biochemistry / Year: 2000
Title: Structural and biochemical characterization of recombinant wild type and a C30A mutant of trimethylamine dehydrogenase from methylophilus methylotrophus (sp. W(3)A(1)).
Authors: Trickey, P. / Basran, J. / Lian, L.Y. / Chen, Z. / Barton, J.D. / Sutcliffe, M.J. / Scrutton, N.S. / Mathews, F.S.
#1: 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. / Mathews, F.S.
History
DepositionDec 3, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)165,6188
Polymers163,1482
Non-polymers2,4706
Water11,908661
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16250 Å2
ΔGint-98 kcal/mol
Surface area45090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.090, 72.000, 83.760
Angle α, β, γ (deg.)90.00, 97.77, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a dimer related by a molecular 2-fold axis.

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Components

#1: Protein TRIMETHYLAMINE DEHYDROGENASE


Mass: 81573.961 Da / Num. of mol.: 2 / Mutation: C30A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylophilus methylotrophus (bacteria)
Strain: W3A1 / Plasmid: PKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): M13MP18 / 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.: 661 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop, microseeding / pH: 6.5
Details: PEG 8000, phosphate buffer, sodium chloride, pH 6.5, vapor diffusion,hanging drop and microseeding, temperature 295.0K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Nov 21, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.22→10 Å / Num. all: 86826 / Num. obs: 81611 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 22.2
Reflection shellResolution: 2.22→2.32 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.123 / Num. unique all: 17184 / % possible all: 71.7
Reflection
*PLUS
Lowest resolution: 50 Å
Reflection shell
*PLUS
% possible obs: 71.7 % / Mean I/σ(I) obs: 6.4

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Processing

Software
NameVersionClassification
X-PLOR3.843refinement
SDMSdata reduction
SDMSdata scaling
RefinementResolution: 2.2→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.187 7871 -RANDOM
Rwork0.139 ---
all-79975 --
obs-78493 98.1 %-
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11480 0 132 661 12273
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.56

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