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- PDB-6a3i: Levoglucosan dehydrogenase, complex with NADH and levoglucosan -

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Basic information

Entry
Database: PDB / ID: 6a3i
TitleLevoglucosan dehydrogenase, complex with NADH and levoglucosan
ComponentsPutative dehydrogenase
KeywordsOXIDOREDUCTASE / NADH-dependent dehydrogenase / Rossmann Fold / Gfo/Idh/MocA family
Function / homology
Function and homology information


levoglucosan dehydrogenase / oxidoreductase activity / nucleotide binding
Similarity search - Function
: / : / GFO/IDH/MocA C-terminal domain / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily ...: / : / GFO/IDH/MocA C-terminal domain / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Levoglucosan / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Levoglucosan dehydrogenase
Similarity search - Component
Biological speciesPseudarthrobacter phenanthrenivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsSugiura, M. / Yamada, C. / Arakawa, T. / Fushinobu, S.
Citation
Journal: J. Biol. Chem. / Year: 2018
Title: Identification, functional characterization, and crystal structure determination of bacterial levoglucosan dehydrogenase.
Authors: Sugiura, M. / Nakahara, M. / Yamada, C. / Arakawa, T. / Kitaoka, M. / Fushinobu, S.
#1: Journal: Biosci. Biotechnol. Biochem. / Year: 1994
Title: Levoglucosan dehydrogenase involved in the assimilation of levoglucosan in Arthrobacter sp. I-552.
Authors: Nakahara, K. / Kitamura, Y. / Yamagishi, Y. / Shoun, H. / Yasui, T.
History
DepositionJun 15, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 21, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 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

Downloads & links

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Assembly

Deposited unit
A: Putative dehydrogenase
B: Putative dehydrogenase
C: Putative dehydrogenase
D: Putative dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,6599
Polymers177,3394
Non-polymers2,3215
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18100 Å2
ΔGint-86 kcal/mol
Surface area45440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.725, 92.354, 100.563
Angle α, β, γ (deg.)90.00, 104.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative dehydrogenase


Mass: 44334.703 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudarthrobacter phenanthrenivorans (strain DSM 18606 / JCM 16027 / LMG 23796 / Sphe3) (bacteria)
Strain: DSM 18606 / JCM 16027 / LMG 23796 / Sphe3 / Gene: Asphe3_10730 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): C43 (DE3) / References: UniProt: F0M433
#2: Chemical ChemComp-4PW / Levoglucosan / (1R,2S,3S,4R,5R)-6,8-dioxabicyclo[3.2.1]octane-2,3,4-triol


Mass: 162.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 1.95 Å3/Da / Density % sol: 37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: MES-NaOH, PEG 3000, PEG 200, NADH, levoglucosan

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 5, 2016
RadiationMonochromator: Cryo-cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 51934 / % possible obs: 99.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 16.1
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2590 / CC1/2: 0.959 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H3V

4h3v


Resolution: 2.41→34.84 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.894 / SU B: 14.636 / SU ML: 0.327 / Cross valid method: THROUGHOUT / ESU R: 0.998 / ESU R Free: 0.354 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29705 2618 5 %RANDOM
Rwork0.21452 ---
obs0.21861 49298 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 63.786 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.01 Å2
2---0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.41→34.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11366 0 91 61 11518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01411746
X-RAY DIFFRACTIONr_bond_other_d0.0030.01710376
X-RAY DIFFRACTIONr_angle_refined_deg1.2481.65815969
X-RAY DIFFRACTIONr_angle_other_deg0.8161.64124244
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.68351465
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.61921.839620
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.569151789
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4461580
X-RAY DIFFRACTIONr_chiral_restr0.0570.21554
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213350
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022249
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_it4.446.535890
X-RAY DIFFRACTIONr_mcbond_other4.446.5295889
X-RAY DIFFRACTIONr_mcangle_it6.4799.7867345
X-RAY DIFFRACTIONr_mcangle_other6.4789.7877346
X-RAY DIFFRACTIONr_scbond_it3.9566.6545856
X-RAY DIFFRACTIONr_scbond_other3.9496.6545848
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8189.9038612
X-RAY DIFFRACTIONr_long_range_B_refined8.45976.9313114
X-RAY DIFFRACTIONr_long_range_B_other8.45976.92813114
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.409→2.472 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 158 -
Rwork0.284 3191 -
obs--86.49 %

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