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- PDB-5itg: Crystal structure of D-sorbitol dehydrogenase in substrate-free form -

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Basic information

Entry
Database: PDB / ID: 5itg
TitleCrystal structure of D-sorbitol dehydrogenase in substrate-free form
ComponentsSorbitol dehydrogenase
KeywordsOXIDOREDUCTASE / Dehydrogenase / Rossmann-fold / L-sorbose / NADPH cofactor
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
Mannitol dehydrogenase / Mannitol dehydrogenase, N-terminal / Mannitol dehydrogenase Rossmann domain / Mannitol dehydrogenase, C-terminal / Mannitol dehydrogenase C-terminal domain / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold ...Mannitol dehydrogenase / Mannitol dehydrogenase, N-terminal / Mannitol dehydrogenase Rossmann domain / Mannitol dehydrogenase, C-terminal / Mannitol dehydrogenase C-terminal domain / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Sorbitol dehydrogenase
Similarity search - Component
Biological speciesGluconobacter oxydans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsJung, W.S. / Pan, C.H.
CitationJournal: Sci Rep / Year: 2016
Title: A highly efficient sorbitol dehydrogenase from Gluconobacter oxydans G624 and improvement of its stability through immobilization
Authors: Kim, T.S. / Patel, S.K. / Selvaraj, C. / Jung, W.S. / Pan, C.H. / Kang, Y.C. / Lee, J.K.
History
DepositionMar 16, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sorbitol dehydrogenase
B: Sorbitol dehydrogenase


Theoretical massNumber of molelcules
Total (without water)108,3092
Polymers108,3092
Non-polymers00
Water5,044280
1
A: Sorbitol dehydrogenase


Theoretical massNumber of molelcules
Total (without water)54,1551
Polymers54,1551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sorbitol dehydrogenase


Theoretical massNumber of molelcules
Total (without water)54,1551
Polymers54,1551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.996, 72.996, 97.269
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 Sorbitol dehydrogenase / D-sorbitol dehyderogenase


Mass: 54154.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gluconobacter oxydans (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9KWR5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.44 Å3/Da / Density % sol: 49.67 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: PEG3350, magnesium chloride, HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 75784 / % possible obs: 96.7 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.084 / Χ2: 1.025 / Net I/σ(I): 9.3 / Num. measured all: 1052126
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.95-1.98120.37329230.733175
1.98-2.0213.20.31836740.734195.6
2.02-2.0613.80.2837090.76196.3
2.06-2.113.80.2437840.776196.9
2.1-2.1513.80.21437410.799197.3
2.15-2.213.80.1937730.818197.4
2.2-2.2513.80.16837900.858197.7
2.25-2.3113.90.15537870.878197.7
2.31-2.3813.90.13638330.904198
2.38-2.46140.12938080.927198.6
2.46-2.54140.11738500.971198.2
2.54-2.6514.20.10738291.005198.4
2.65-2.7714.20.09838581.048198.9
2.77-2.9114.20.08938791.092198.9
2.91-3.114.30.08138571.134198.9
3.1-3.3314.40.07439121.198199.1
3.33-3.6714.60.06739211.227199
3.67-4.214.40.06139361.277199
4.2-5.2914.10.0639681.348198.7
5.29-5012.70.07439521.837193.9

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Processing

Software
NameVersionClassification
CNSrefinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data processing
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→50 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2531 7281 9.3 %
Rwork0.2165 64747 -
obs-72028 92.3 %
Solvent computationBsol: 49.9008 Å2
Displacement parametersBiso max: 78.04 Å2 / Biso mean: 26.9518 Å2 / Biso min: 2.92 Å2
Baniso -1Baniso -2Baniso -3
1-6.411 Å20 Å20 Å2
2---2.117 Å20 Å2
3----4.294 Å2
Refinement stepCycle: final / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7544 0 280 0 7824
Biso mean--25.92 --
Num. residues----968
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.177
X-RAY DIFFRACTIONc_mcbond_it1.2931.5
X-RAY DIFFRACTIONc_scbond_it2.1792
X-RAY DIFFRACTIONc_mcangle_it1.92
X-RAY DIFFRACTIONc_scangle_it3.0652.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-2.020.25535710.2135083565473.6
2.02-2.10.27046420.22396004664686.3
2.1-2.20.26137070.21436194690189.5
2.2-2.310.26797400.21316411715192.3
2.31-2.460.27587420.22056539728194.5
2.46-2.650.26437670.22666659742695.5
2.65-2.910.28587270.23816885761297.5
2.91-3.330.26147830.23046902768598.4
3.33-4.20.23377950.20747006780198.8
4.2-500.22998070.20127064787196.2
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.param

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