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- PDB-4mkx: Crystal Structure of apo scyllo-inositol dehydrogenase from Lacto... -

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Basic information

Entry
Database: PDB / ID: 4mkx
TitleCrystal Structure of apo scyllo-inositol dehydrogenase from Lactobacillus casei
ComponentsInositol dehydrogenase
KeywordsOXIDOREDUCTASE / NAD / sugar alcohol dehydrogenases / Rossmann fold / dehydrogenase / scyllo-inositol / dehydrogenate
Function / homology
Function and homology information


NADPH regeneration / oxidoreductase activity / nucleotide binding / cytoplasm
Similarity search - Function
Inositol 2-dehydrogenase / : / 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 ...Inositol 2-dehydrogenase / : / 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
Inositol dehydrogenase
Similarity search - Component
Biological speciesLactobacillus casei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsBertwistle, D. / Linda, V. / Sanders, D.A.R. / Palmer, D.R.J.
CitationJournal: To be Published
Title: Crystal Structure of apo scyllo-inositol dehydrogenase from Lactobacillus casei
Authors: Bertwistle, D. / Aamudalapalli, H. / Vogt, L. / Sanders, D.A.R. / Palmer, D.R.J.
History
DepositionSep 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inositol dehydrogenase


Theoretical massNumber of molelcules
Total (without water)39,0801
Polymers39,0801
Non-polymers00
Water2,252125
1
A: Inositol dehydrogenase

A: Inositol dehydrogenase

A: Inositol dehydrogenase

A: Inositol dehydrogenase


Theoretical massNumber of molelcules
Total (without water)156,3214
Polymers156,3214
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area13790 Å2
ΔGint-93 kcal/mol
Surface area49650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.920, 123.330, 132.120
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-473-

HOH

21A-489-

HOH

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Components

#1: Protein Inositol dehydrogenase / Scyllo-inositol dehydrogenase


Mass: 39080.344 Da / Num. of mol.: 1
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: A5YBJ8, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.29 Å3/Da / Density % sol: 46.26 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 5
Details: 1:1 2.8 M ammonium sulfate + 0.18 M citric acid, pH 5.0 to 25 mM Tris-Hcl, pH 8.0, MICROBATCH, temperature 298K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97952 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 26, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97952 Å / Relative weight: 1
ReflectionResolution: 1.6→90.155 Å / Num. all: 47857 / Num. obs: 47857 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 19.23 Å2 / Rsym value: 0.076 / Net I/σ(I): 12.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.6-1.697.20.5631.15015369220.563100
1.69-1.797.30.381.74766065260.38100
1.79-1.917.30.2352.84510761490.235100
1.91-2.077.40.1594.14239657570.159100
2.07-2.267.40.10963894352860.109100
2.26-2.537.40.0936.83553648110.093100
2.53-2.927.40.0966.33154042770.096100
2.92-3.587.30.0619.62667436330.061100
3.58-5.067.20.046132068228560.046100
5.06-35.0656.80.04313.61112316400.04399.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
MOLREPphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
MxDCdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→35.065 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8161 / SU ML: 0.18 / σ(F): 1.35 / Phase error: 25.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2262 2424 5.07 %RANDOM
Rwork0.2011 ---
obs0.2023 47835 99.92 %-
all-47857 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 61.11 Å2 / Biso mean: 20.3408 Å2 / Biso min: 5.7 Å2
Refinement stepCycle: LAST / Resolution: 1.6→35.065 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2619 0 0 125 2744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062663
X-RAY DIFFRACTIONf_angle_d1.0723596
X-RAY DIFFRACTIONf_chiral_restr0.074410
X-RAY DIFFRACTIONf_plane_restr0.005468
X-RAY DIFFRACTIONf_dihedral_angle_d14.265973
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.63270.3241380.296426582796100
1.6327-1.66820.34721490.277526142763100
1.6682-1.7070.31171360.278226092745100
1.707-1.74970.2981520.263726622814100
1.7497-1.7970.26021370.253226232760100
1.797-1.84990.28461560.244926282784100
1.8499-1.90960.29821460.237226612807100
1.9096-1.97780.26881280.232326572785100
1.9778-2.0570.24311340.222326482782100
2.057-2.15060.25911290.2226882817100
2.1506-2.2640.24221490.206426392788100
2.264-2.40580.22821370.201226722809100
2.4058-2.59150.19741340.208427082842100
2.5915-2.85220.23811460.205126602806100
2.8522-3.26460.2181660.197126792845100
3.2646-4.11210.18491340.160927592893100
4.1121-35.07330.18471530.1692846299999

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