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- PDB-5b37: Crystal structure of L-tryptophan dehydrogenase from Nostoc punct... -

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Basic information

Entry
Database: PDB / ID: 5b37
TitleCrystal structure of L-tryptophan dehydrogenase from Nostoc punctiforme
ComponentsTryptophan dehydrogenase
KeywordsOXIDOREDUCTASE / dehydrogenase
Function / homology
Function and homology information


tryptophan dehydrogenase / tryptophan dehydrogenase activity / amino acid metabolic process / nucleotide binding
Similarity search - Function
Glutamate/phenylalanine/leucine/valine dehydrogenase, bacterial/archaeal / Leucine Dehydrogenase, chain A, domain 1 / Leu/Phe/Val dehydrogenases active site / Glu / Leu / Phe / Val dehydrogenases active site. / Glutamate/phenylalanine/leucine/valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain / Glu/Leu/Phe/Val dehydrogenase, dimerisation domain / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase ...Glutamate/phenylalanine/leucine/valine dehydrogenase, bacterial/archaeal / Leucine Dehydrogenase, chain A, domain 1 / Leu/Phe/Val dehydrogenases active site / Glu / Leu / Phe / Val dehydrogenases active site. / Glutamate/phenylalanine/leucine/valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain / Glu/Leu/Phe/Val dehydrogenase, dimerisation domain / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Tryptophan dehydrogenase
Similarity search - Component
Biological speciesNostoc punctiforme NIES-2108 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsWakamatsu, T. / Sakuraba, H. / Kitamura, M. / Hakumai, Y. / Ohnishi, K. / Ashiuchi, M. / Ohshima, T.
CitationJournal: Appl. Environ. Microbiol. / Year: 2017
Title: Structural Insights into l-Tryptophan Dehydrogenase from a Photoautotrophic Cyanobacterium, Nostoc punctiforme.
Authors: Wakamatsu, T. / Sakuraba, H. / Kitamura, M. / Hakumai, Y. / Fukui, K. / Ohnishi, K. / Ashiuchi, M. / Ohshima, T.
History
DepositionFeb 11, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Derived calculations
Revision 1.2Dec 6, 2017Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tryptophan dehydrogenase
B: Tryptophan dehydrogenase
C: Tryptophan dehydrogenase
D: Tryptophan dehydrogenase
E: Tryptophan dehydrogenase
F: Tryptophan dehydrogenase


Theoretical massNumber of molelcules
Total (without water)237,5416
Polymers237,5416
Non-polymers00
Water50428
1
A: Tryptophan dehydrogenase

B: Tryptophan dehydrogenase


Theoretical massNumber of molelcules
Total (without water)79,1802
Polymers79,1802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_454x-1,y,z-11
Buried area2320 Å2
ΔGint-8 kcal/mol
Surface area30170 Å2
MethodPISA
2
C: Tryptophan dehydrogenase

F: Tryptophan dehydrogenase


Theoretical massNumber of molelcules
Total (without water)79,1802
Polymers79,1802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area2490 Å2
ΔGint-6 kcal/mol
Surface area30450 Å2
MethodPISA
3
D: Tryptophan dehydrogenase

E: Tryptophan dehydrogenase


Theoretical massNumber of molelcules
Total (without water)79,1802
Polymers79,1802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area2490 Å2
ΔGint-12 kcal/mol
Surface area30880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.713, 337.766, 63.646
Angle α, β, γ (deg.)90.00, 120.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Tryptophan dehydrogenase /


Mass: 39590.113 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc punctiforme NIES-2108 (bacteria)
Plasmid: pET-29b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami2(DE3)pLysS / References: UniProt: W8CV45, tryptophan dehydrogenase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES-NaOH (pH 7.5), polyethylene glycol 8000, ethylene glycol

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.18
11-H, -K, H+L20.144
11H+L, -K, -L30.194
11L, K, -H-L40.167
11-H-L, K, H50.159
11L, -K, H60.157
ReflectionResolution: 3.4→50 Å / Num. obs: 88938 / % possible obs: 99.1 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 8.3
Reflection shellResolution: 3.4→3.46 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VPX

3vpx


Resolution: 3.4→50 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.864 / SU B: 16.191 / SU ML: 0.277 / Cross valid method: THROUGHOUT / ESU R Free: 0.133
Details: THE STRUCTURE WAS ORIGINALLY REFINED USING P61 2 2, THE R/RFREE VALUES WAS HIGH. THE STRUCTURE WAS THEN REFINED USING P21, THE R/RFREE VALUES WAS DECREASED DRAMATICALLY. HYDROGENS HAVE BEEN ...Details: THE STRUCTURE WAS ORIGINALLY REFINED USING P61 2 2, THE R/RFREE VALUES WAS HIGH. THE STRUCTURE WAS THEN REFINED USING P21, THE R/RFREE VALUES WAS DECREASED DRAMATICALLY. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25418 1494 4.7 %RANDOM
Rwork0.20273 ---
obs0.20498 30208 98.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 96.801 Å2
Baniso -1Baniso -2Baniso -3
1-193.87 Å2-0 Å2-86.62 Å2
2---78.65 Å2-0 Å2
3----115.22 Å2
Refinement stepCycle: 1 / Resolution: 3.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15375 0 0 28 15403
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01915623
X-RAY DIFFRACTIONr_bond_other_d0.0060.0215308
X-RAY DIFFRACTIONr_angle_refined_deg1.1771.96121132
X-RAY DIFFRACTIONr_angle_other_deg0.915335138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.74651977
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.33624.681705
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.485152716
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0561595
X-RAY DIFFRACTIONr_chiral_restr0.0660.22440
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217774
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023481
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.3479.6737965
X-RAY DIFFRACTIONr_mcbond_other4.3479.6737964
X-RAY DIFFRACTIONr_mcangle_it6.34814.5149923
X-RAY DIFFRACTIONr_mcangle_other6.34814.5149924
X-RAY DIFFRACTIONr_scbond_it5.459.8927658
X-RAY DIFFRACTIONr_scbond_other5.459.8927658
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.52614.73811210
X-RAY DIFFRACTIONr_long_range_B_refined8.01176.00317160
X-RAY DIFFRACTIONr_long_range_B_other8.01276.00317160
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.385→3.473 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 104 -
Rwork0.217 1996 -
obs--87.87 %

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