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- PDB-7d5n: Crystal structure of inositol dehydrogenase homolog complexed wit... -

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Basic information

Entry
Database: PDB / ID: 7d5n
TitleCrystal structure of inositol dehydrogenase homolog complexed with NADH and myo-inositol from Azotobacter vinelandii
ComponentsOxidoreductase
KeywordsOXIDOREDUCTASE / Complex
Function / homology
Function and homology information


: / Gfo/Idh/MocA-like oxidoreductase, C-terminal / 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 domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Oxidoreductase
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFukano, K. / Ono, T. / Suzuki, M. / Takenoya, M. / Ito, S. / Sasaki, Y. / Yajima, S.
CitationJournal: To Be Published
Title: Crystal structure of inositol dehydrogenase complexed with NADH and myo-inositol from Azotobacter vinelandii
Authors: Fukano, K. / Ono, T. / Suzuki, M. / Takenoya, M. / Ito, S. / Sasaki, Y. / Yajima, S.
History
DepositionSep 27, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oxidoreductase
B: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4285
Polymers88,9172
Non-polymers1,5113
Water4,918273
1
A: Oxidoreductase
B: Oxidoreductase
hetero molecules

A: Oxidoreductase
B: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,85510
Polymers177,8334
Non-polymers3,0226
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area19940 Å2
ΔGint-102 kcal/mol
Surface area49660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.810, 151.530, 48.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Oxidoreductase


Mass: 44458.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (strain DJ / ATCC BAA-1303) (bacteria)
Strain: DJ / ATCC BAA-1303 / Gene: Avin_50260 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C1DLC3
#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical ChemComp-INS / 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE / MYO-INOSITOL


Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.04 Å3/Da / Density % sol: 39.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ca acetate, 14% PEG3350,10 mM NADH, 50 mM myo-inositol

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 63455 / % possible obs: 92.5 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Net I/σ(I): 19.9
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.558 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2999 / CC1/2: 0.788 / % possible all: 59.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DTY

3dty


Resolution: 1.8→48.166 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.679 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.12
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1969 3177 5.007 %
Rwork0.1794 60278 -
all0.18 --
obs-63455 92.482 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.458 Å20 Å20 Å2
2---0.964 Å20 Å2
3---0.506 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.166 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5972 0 100 273 6345
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0136223
X-RAY DIFFRACTIONr_bond_other_d0.0020.0175632
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.6598445
X-RAY DIFFRACTIONr_angle_other_deg1.4991.58412973
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8975764
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5820.466365
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.24415963
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0471563
X-RAY DIFFRACTIONr_chiral_restr0.0760.2756
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027109
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021460
X-RAY DIFFRACTIONr_nbd_refined0.2010.21252
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.25413
X-RAY DIFFRACTIONr_nbtor_refined0.1650.23036
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.22681
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2228
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2780.234
X-RAY DIFFRACTIONr_nbd_other0.2480.283
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0930.29
X-RAY DIFFRACTIONr_mcbond_it1.4382.2483068
X-RAY DIFFRACTIONr_mcbond_other1.4352.2473067
X-RAY DIFFRACTIONr_mcangle_it2.1453.3613828
X-RAY DIFFRACTIONr_mcangle_other2.1453.3613829
X-RAY DIFFRACTIONr_scbond_it2.1442.5433154
X-RAY DIFFRACTIONr_scbond_other2.1442.5433155
X-RAY DIFFRACTIONr_scangle_it3.4523.7094616
X-RAY DIFFRACTIONr_scangle_other3.4513.7094617
X-RAY DIFFRACTIONr_lrange_it4.32626.2246968
X-RAY DIFFRACTIONr_lrange_other4.32426.1936936
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.2971710.2582822X-RAY DIFFRACTION59.5503
1.847-1.8970.261630.2273164X-RAY DIFFRACTION68.7965
1.897-1.9520.2391790.2313581X-RAY DIFFRACTION79.1079
1.952-2.0120.2151940.2094096X-RAY DIFFRACTION92.2978
2.012-2.0780.2362420.2024208X-RAY DIFFRACTION99.8653
2.078-2.1510.2162190.1914043X-RAY DIFFRACTION99.0242
2.151-2.2320.1982030.1833958X-RAY DIFFRACTION99.1186
2.232-2.3230.2092090.1743802X-RAY DIFFRACTION99.3068
2.323-2.4270.2051960.1823666X-RAY DIFFRACTION99.3824
2.427-2.5450.2061780.1813525X-RAY DIFFRACTION99.4361
2.545-2.6830.1951800.1783353X-RAY DIFFRACTION99.5211
2.683-2.8450.1891540.183207X-RAY DIFFRACTION99.7329
2.845-3.0410.1751570.1852974X-RAY DIFFRACTION99.7134
3.041-3.2850.1921480.1822784X-RAY DIFFRACTION99.694
3.285-3.5970.1761520.1752579X-RAY DIFFRACTION99.7079
3.597-4.0210.1711290.1532364X-RAY DIFFRACTION99.5607
4.021-4.6410.184990.1392096X-RAY DIFFRACTION99.6821
4.641-5.680.186910.171794X-RAY DIFFRACTION99.4198
5.68-8.0140.208690.1761424X-RAY DIFFRACTION99.3347
8.014-48.1660.186440.195838X-RAY DIFFRACTION98.2183

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