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- PDB-1djn: STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF RECOMBINANT WILD T... -

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Basic information

Entry
Database: PDB / ID: 1djn
TitleSTRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF RECOMBINANT WILD TYPE TRIMETHYLAMINE DEHYDROGENASE FROM METHYLOPHILUS METHYLOTROPHUS (SP. W3A1)
ComponentsTRIMETHYLAMINE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / IRON-SULFUR FLAVOPROTEIN / ELECTRON TRANSFER
Function / homologyAldolase-type TIM barrel / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain superfamily / Trimethylamine dehydrogenase/Dimethylamine dehydrogenase, FMN-binding domain / NADH:flavin oxidoreductase / NADH oxidase family / Pyridine nucleotide-disulphide oxidoreductase / trimethylamine dehydrogenase / trimethylamine dehydrogenase activity / 4 iron, 4 sulfur cluster binding ...Aldolase-type TIM barrel / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain superfamily / Trimethylamine dehydrogenase/Dimethylamine dehydrogenase, FMN-binding domain / NADH:flavin oxidoreductase / NADH oxidase family / Pyridine nucleotide-disulphide oxidoreductase / trimethylamine dehydrogenase / trimethylamine dehydrogenase activity / 4 iron, 4 sulfur cluster binding / FMN binding / metal ion binding / Trimethylamine dehydrogenase
Function and homology information
Specimen sourceMethylophilus methylotrophus (bacteria)
MethodX-RAY DIFFRACTION / 2.2 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 3, 1999 / Release: Dec 22, 1999
RevisionDateData content typeGroupCategoryProviderType
1.0Dec 22, 1999Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelSource and taxonomy / Version format compliance
1.3Oct 4, 2017Structure modelRefinement descriptionsoftware

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)165,6828
Polyers163,2122
Non-polymers2,4706
Water11,764653
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)16100
ΔGint (kcal/M)-95
Surface area (Å2)45300
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)148.160, 72.000, 83.810
Angle α, β, γ (deg.)90.00, 97.73, 90.00
Int Tables number4
Space group name H-MP 1 21 1

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Components

#1: Protein/peptide TRIMETHYLAMINE DEHYDROGENASE /


Mass: 81606.023 Da / Num. of mol.: 2
Source: (gene. exp.) Methylophilus methylotrophus (bacteria)
Genus: Methylophilus / Species: Methylophilus methylotrophus / Strain: W3A1 / Plasmid name: PKK223-3 / Genus (production host): Escherichia / 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 / Formula: Fe4S4 / Iron–sulfur cluster
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Formula: C17H21N4O9P / Flavin mononucleotide
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 653 / Formula: H2O / Water

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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 / Density percent sol: 54.66 %
Crystal growTemp: 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 295K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop

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Data collection

DiffractionMean temperature: 298 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Collection date: Dec 3, 1995
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 18 Å2 / D resolution high: 2.22 Å / D resolution low: 1 Å / Number all: 86785 / Number obs: 81423 / Observed criterion sigma F: 0 / Observed criterion sigma I: 0 / Rmerge I obs: 0.052 / NetI over sigmaI: 17 / Redundancy: 3.2 % / Percent possible obs: 93.8
Reflection shellRmerge I obs: 0.132 / Highest resolution: 2.22 Å / Lowest resolution: 2.32 Å / Redundancy: 2 % / Percent possible all: 70.9
Reflection
*PLUS
D resolution low: 5 Å
Reflection shell
*PLUS
Percent possible obs: 70.9 / Redundancy: 2.2 % / MeanI over sigI obs: 4.4

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Processing

Software
NameVersionClassification
X-PLOR3.843refinement
SDMSdata reduction
SDMSdata scaling
RefineR Free selection details: RANDOM / Sigma F: 2 / Stereochemistry target values: ENGH & HUBER
Least-squares processR factor R free: 0.185 / R factor R work: 0.139 / R factor obs: 0.139 / Highest resolution: 2.2 Å / Lowest resolution: 8 Å / Number reflection R free: 7740 / Number reflection all: 79791 / Number reflection obs: 77367 / Percent reflection obs: 97
Refine hist #LASTHighest resolution: 2.2 Å / Lowest resolution: 8 Å
Number of atoms included #LASTProtein: 11482 / Nucleic acid: 0 / Ligand: 132 / Solvent: 653 / Total: 12267
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_deg1.40
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

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