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- PDB-7d5m: Crystal structure of inositol dehydrogenase homolog complexed wit... -

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Basic information

Entry
Database: PDB / ID: 7d5m
TitleCrystal structure of inositol dehydrogenase homolog complexed with NAD+ 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Oxidoreductase
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 NAD+ 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7952
Polymers44,1321
Non-polymers6631
Water4,918273
1
A: Oxidoreductase
hetero molecules

A: Oxidoreductase
hetero molecules

A: Oxidoreductase
hetero molecules

A: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,1818
Polymers176,5274
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area18930 Å2
ΔGint-111 kcal/mol
Surface area51040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.250, 107.997, 156.759
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-691-

HOH

21A-699-

HOH

31A-833-

HOH

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Components

#1: Protein Oxidoreductase


Mass: 44131.867 Da / Num. of mol.: 1
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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


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

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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: 2.6 Å3/Da / Density % sol: 52.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M ammonium tartrate dibasic, pH 7.0, 12% (w/v) PEG 3350, 10 mM NAD+

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 46835 / % possible obs: 99.7 % / Redundancy: 3.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.041 / Net I/σ(I): 33.1
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 6 / Num. unique obs: 2284 / CC1/2: 0.95

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DTY

3dty


Resolution: 1.75→37.663 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.843 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.094
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1933 2274 4.857 %
Rwork0.1789 44543 -
all0.18 --
obs-46817 99.541 %
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: 15.538 Å2
Baniso -1Baniso -2Baniso -3
1-1.523 Å20 Å20 Å2
2---0.83 Å20 Å2
3----0.692 Å2
Refinement stepCycle: LAST / Resolution: 1.75→37.663 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3027 0 44 273 3344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0133148
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172840
X-RAY DIFFRACTIONr_angle_refined_deg1.3371.644272
X-RAY DIFFRACTIONr_angle_other_deg1.3831.5726546
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0265388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43220.538186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.50215490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1271532
X-RAY DIFFRACTIONr_chiral_restr0.070.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023624
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02731
X-RAY DIFFRACTIONr_nbd_refined0.1970.2635
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.22729
X-RAY DIFFRACTIONr_nbtor_refined0.1610.21512
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21375
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2189
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2440.213
X-RAY DIFFRACTIONr_nbd_other0.2080.270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0850.219
X-RAY DIFFRACTIONr_mcbond_it0.821.5341555
X-RAY DIFFRACTIONr_mcbond_other0.821.5341554
X-RAY DIFFRACTIONr_mcangle_it1.3382.2971942
X-RAY DIFFRACTIONr_mcangle_other1.3372.2981943
X-RAY DIFFRACTIONr_scbond_it1.3661.7231591
X-RAY DIFFRACTIONr_scbond_other1.3661.7231592
X-RAY DIFFRACTIONr_scangle_it2.1192.5232330
X-RAY DIFFRACTIONr_scangle_other2.1182.5232331
X-RAY DIFFRACTIONr_lrange_it3.10318.3853572
X-RAY DIFFRACTIONr_lrange_other3.0318.1383519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.748-1.7940.2211640.2073157X-RAY DIFFRACTION97.1337
1.794-1.8430.2291630.2013186X-RAY DIFFRACTION99.9403
1.843-1.8960.221360.2243130X-RAY DIFFRACTION99.7252
1.896-1.9540.2271560.2062996X-RAY DIFFRACTION100
1.954-2.0190.241580.1852932X-RAY DIFFRACTION100
2.019-2.0890.1911560.1752806X-RAY DIFFRACTION100
2.089-2.1680.1861370.172739X-RAY DIFFRACTION99.9652
2.168-2.2570.2261250.1912623X-RAY DIFFRACTION99.9273
2.257-2.3570.2191350.1762546X-RAY DIFFRACTION99.7025
2.357-2.4720.1931310.1692413X-RAY DIFFRACTION100
2.472-2.6050.1881080.1642305X-RAY DIFFRACTION99.9586
2.605-2.7630.1911140.1672170X-RAY DIFFRACTION100
2.763-2.9540.1931190.1692038X-RAY DIFFRACTION99.8611
2.954-3.190.163990.1841962X-RAY DIFFRACTION99.8547
3.19-3.4940.219940.181739X-RAY DIFFRACTION99.9455
3.494-3.9060.17680.1711643X-RAY DIFFRACTION99.7086
3.906-4.5090.139780.1461437X-RAY DIFFRACTION99.7367
4.509-5.5190.157620.1771220X-RAY DIFFRACTION99.5342
5.519-7.790.229440.186976X-RAY DIFFRACTION99.5122
7.79-37.6630.179270.21526X-RAY DIFFRACTION90.6557

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