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- PDB-4n54: Crystal structure of scyllo-inositol dehydrogenase from Lactobaci... -

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Basic information

Entry
Database: PDB / ID: 4n54
TitleCrystal structure of scyllo-inositol dehydrogenase from Lactobacillus casei with bound cofactor NAD(H) and scyllo-inositol
ComponentsInositol dehydrogenase
KeywordsOXIDOREDUCTASE / hydrogen bonding / NAD / sugar alcohol dehydrogenases / Rossmann fold / dehydrogenate
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity / nucleotide binding
Similarity search - Function
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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich ...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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(1r,2r,3r,4r,5r,6r)-cyclohexane-1,2,3,4,5,6-hexol / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Inositol dehydrogenase / :
Similarity search - Component
Biological speciesLactobacillus casei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsBertwistle, D. / Sanders, D.A.R. / Palmer, D.R.J.
CitationJournal: To be Published
Title: Crystal structure of scyllo-inositol dehydrogenase from Lactobacillus casei with bound cofactor NAD(H) and scyllo-inositol
Authors: Bertwistle, D. / Aamudalapalli, H. / Sanders, D.A.R. / Palmer, D.R.J.
History
DepositionOct 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)158,08211
Polymers154,8804
Non-polymers3,2027
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18460 Å2
ΔGint-131 kcal/mol
Surface area46490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.250, 99.830, 192.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Inositol dehydrogenase / Scyllo-inositol dehydrogenase


Mass: 38719.918 Da / Num. of mol.: 4 / Fragment: UNP residues 4-343
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus casei (bacteria) / Strain: BL23 / Gene: idh, iolG, iolG2, LCABL_02220 / Plasmid: pQE-80L / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue
References: UniProt: B3W8L4, UniProt: A0A0J9X1Y7*PLUS, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical ChemComp-2H3 / (1r,2r,3r,4r,5r,6r)-cyclohexane-1,2,3,4,5,6-hexol / scyllo-inositol / Scyllo-Inositol


Mass: 180.156 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H12O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.64 Å3/Da / Density % sol: 53.49 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 7.5
Details: 0.1 M magnesium chloride, 0.050 M HEPES pH 7.5, 15% w/v PEG400, 0.0125 M Tris-HCl, pH 8.0, MICROBATCH, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97959 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 26, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97959 Å / Relative weight: 1
ReflectionResolution: 2.05→96.255 Å / Num. all: 100263 / Num. obs: 100263 / % possible obs: 96.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 32.01 Å2 / Rsym value: 0.14 / Net I/σ(I): 7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.05-2.166.30.7770.90.777195.1
2.16-2.296.20.5361.30.536195.3
2.29-2.456.20.4131.70.413195.6
2.45-2.656.10.3082.30.308196
2.65-2.960.2073.20.207196.7
2.9-3.245.90.1653.70.165198.2
3.24-3.7460.1334.50.133199.3
3.74-4.586.30.1055.60.105199.7
4.58-6.486.80.0965.90.096199.9
6.48-45.6066.80.0678.40.067199.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
MOLREPphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
MxDCdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4KMX

4kmx


Resolution: 2.05→45.606 Å / Occupancy max: 1 / Occupancy min: 0.39 / SU ML: 0.16 / σ(F): 1.33 / Phase error: 27.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2611 4998 4.99 %
Rwork0.2222 --
obs0.2244 100073 96.56 %
all-100263 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.349 Å2
Refinement stepCycle: LAST / Resolution: 2.05→45.606 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10504 0 212 183 10899
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01610928
X-RAY DIFFRACTIONf_angle_d1.32914811
X-RAY DIFFRACTIONf_dihedral_angle_d15.3274009
X-RAY DIFFRACTIONf_chiral_restr0.1051708
X-RAY DIFFRACTIONf_plane_restr0.011897
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.07330.351480.30273098X-RAY DIFFRACTION95
2.0733-2.09770.30251790.28593023X-RAY DIFFRACTION95
2.0977-2.12330.30241670.27823098X-RAY DIFFRACTION94
2.1233-2.15010.35141720.27823052X-RAY DIFFRACTION95
2.1501-2.17840.30241480.27893104X-RAY DIFFRACTION95
2.1784-2.20830.34291480.26833070X-RAY DIFFRACTION95
2.2083-2.23980.30681830.26943069X-RAY DIFFRACTION94
2.2398-2.27330.26931610.2613090X-RAY DIFFRACTION95
2.2733-2.30880.33851690.26513077X-RAY DIFFRACTION94
2.3088-2.34660.30941390.26443118X-RAY DIFFRACTION96
2.3466-2.38710.29511700.27163092X-RAY DIFFRACTION94
2.3871-2.43050.33131690.26843107X-RAY DIFFRACTION95
2.4305-2.47720.30391510.27113102X-RAY DIFFRACTION96
2.4772-2.52780.30871760.26323095X-RAY DIFFRACTION95
2.5278-2.58280.27611790.26053089X-RAY DIFFRACTION95
2.5828-2.64280.31661500.26993132X-RAY DIFFRACTION96
2.6428-2.70890.29391320.24993171X-RAY DIFFRACTION96
2.7089-2.78220.28581560.24443149X-RAY DIFFRACTION96
2.7822-2.8640.29121920.2383114X-RAY DIFFRACTION96
2.864-2.95640.28131560.23033172X-RAY DIFFRACTION97
2.9564-3.06210.28611640.253211X-RAY DIFFRACTION97
3.0621-3.18460.26471930.243199X-RAY DIFFRACTION98
3.1846-3.32950.24111630.21353254X-RAY DIFFRACTION99
3.3295-3.5050.24041770.20473236X-RAY DIFFRACTION99
3.505-3.72450.23291670.2013315X-RAY DIFFRACTION99
3.7245-4.0120.22041800.20273285X-RAY DIFFRACTION99
4.012-4.41540.22191610.17733312X-RAY DIFFRACTION99
4.4154-5.05360.22871880.17373345X-RAY DIFFRACTION100
5.0536-6.36420.25721710.20673384X-RAY DIFFRACTION100
6.3642-45.61740.22641890.19663512X-RAY DIFFRACTION99

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