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- PDB-6a3f: Levoglucosan dehydrogenase, apo form -

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Basic information

Entry
Database: PDB / ID: 6a3f
TitleLevoglucosan dehydrogenase, apo form
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 dehydrogenase
Similarity search - Component
Biological speciesPseudarthrobacter phenanthrenivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9585
Polymers88,6692
Non-polymers2883
Water8,719484
1
A: Putative dehydrogenase
B: Putative dehydrogenase
hetero molecules

A: Putative dehydrogenase
B: Putative dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,91510
Polymers177,3394
Non-polymers5766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area16980 Å2
ΔGint-151 kcal/mol
Surface area49640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.649, 95.649, 170.912
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-685-

HOH

21B-675-

HOH

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Components

#1: Protein Putative dehydrogenase


Mass: 44334.703 Da / Num. of mol.: 2
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: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): C43 (DE3) / References: UniProt: F0M433
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / 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: 2.2 Å3/Da / Density % sol: 44.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: sodium cacodylate, ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 28, 2015
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 74076 / % possible obs: 99.9 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 35.4
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.694 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 3610 / CC1/2: 0.974 / % possible all: 100

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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: 1.8→38.28 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.636 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.111 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20192 3758 5.1 %RANDOM
Rwork0.16657 ---
obs0.16839 70139 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.844 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.8→38.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5851 0 15 484 6350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0156009
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175309
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.7568158
X-RAY DIFFRACTIONr_angle_other_deg0.5291.73312406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2675760
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.41720.15266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.56515814
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7151542
X-RAY DIFFRACTIONr_chiral_restr0.0760.2785
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216894
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021154
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_it2.3322.7023052
X-RAY DIFFRACTIONr_mcbond_other2.3322.7043053
X-RAY DIFFRACTIONr_mcangle_it3.1734.0343808
X-RAY DIFFRACTIONr_mcangle_other3.1754.0363809
X-RAY DIFFRACTIONr_scbond_it3.0192.9472957
X-RAY DIFFRACTIONr_scbond_other2.9582.9362946
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.34.3024333
X-RAY DIFFRACTIONr_long_range_B_refined5.2732.8566663
X-RAY DIFFRACTIONr_long_range_B_other5.18732.5766570
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 287 -
Rwork0.21 5069 -
obs--99.72 %

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