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- PDB-3qe3: Sheep liver sorbitol dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 3qe3
TitleSheep liver sorbitol dehydrogenase
ComponentsSorbitol dehydrogenase
KeywordsOXIDOREDUCTASE / medium chain dehydrogenase/reductase enzymes
Function / homology
Function and homology information


D-xylulose reductase / sorbitol catabolic process / D-xylulose reductase activity / L-iditol 2-dehydrogenase / L-iditol 2-dehydrogenase activity / flagellated sperm motility / fructose biosynthetic process / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / motile cilium / mitochondrial membrane ...D-xylulose reductase / sorbitol catabolic process / D-xylulose reductase activity / L-iditol 2-dehydrogenase / L-iditol 2-dehydrogenase activity / flagellated sperm motility / fructose biosynthetic process / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / motile cilium / mitochondrial membrane / NAD binding / protein-containing complex / zinc ion binding
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase ...Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Sorbitol dehydrogenase
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsYennawar, N.H. / Yennawar, H.P.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: X-ray crystal structure and small-angle X-ray scattering of sheep liver sorbitol dehydrogenase.
Authors: Yennawar, H. / Moller, M. / Gillilan, R. / Yennawar, N.
History
DepositionJan 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 27, 2013Group: Database references
Revision 1.3Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Sorbitol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3536
Polymers38,0151
Non-polymers3385
Water3,855214
1
A: Sorbitol dehydrogenase
hetero molecules

A: Sorbitol dehydrogenase
hetero molecules

A: Sorbitol dehydrogenase
hetero molecules

A: Sorbitol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,41024
Polymers152,0604
Non-polymers1,35120
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area13250 Å2
ΔGint-223 kcal/mol
Surface area48440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.749, 85.881, 119.888
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-481-

HOH

21A-533-

HOH

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Components

#1: Protein Sorbitol dehydrogenase / / L-iditol 2-dehydrogenase


Mass: 38014.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ovis aries (sheep) / Gene: SORD / Organ: liver / Production host: Escherichia coli (E. coli) / References: UniProt: P07846, L-iditol 2-dehydrogenase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 46.37 %
Crystal growTemperature: 294 K / Method: laser-induced nucleation, sitting drop / pH: 7
Details: 0.2 M lithium acetate dyhydrate, 20% PEG3350, pH 7.0, LASER-INDUCED NUCLEATION, SITTING DROP, temperature 294.0K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 1, 2010
RadiationMonochromator: Varimax HF optic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 27863 / Num. obs: 27863 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 26
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 3.4 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PL8

1pl8


Resolution: 1.9→20.002 Å / SU ML: 0.25 / σ(F): 1.33 / Phase error: 25.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2343 1391 5.06 %
Rwork0.1923 --
obs0.1945 27476 98.38 %
all-27863 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.681 Å2 / ksol: 0.374 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.0066 Å20 Å2-0 Å2
2--6.4826 Å20 Å2
3----5.476 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20.002 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2638 0 19 214 2871
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082711
X-RAY DIFFRACTIONf_angle_d1.0773676
X-RAY DIFFRACTIONf_dihedral_angle_d11.604998
X-RAY DIFFRACTIONf_chiral_restr0.071422
X-RAY DIFFRACTIONf_plane_restr0.005478
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.96790.3241360.30352553X-RAY DIFFRACTION98
1.9679-2.04660.26711250.22912561X-RAY DIFFRACTION97
2.0466-2.13960.28681400.23112588X-RAY DIFFRACTION99
2.1396-2.25230.27261440.22492562X-RAY DIFFRACTION98
2.2523-2.39320.29351320.22072554X-RAY DIFFRACTION97
2.3932-2.57760.27351370.21332572X-RAY DIFFRACTION99
2.5776-2.83630.26371560.21362604X-RAY DIFFRACTION99
2.8363-3.24530.22021420.19172666X-RAY DIFFRACTION99
3.2453-4.0830.20481180.15782666X-RAY DIFFRACTION99
4.083-20.00290.18411610.15562759X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 20.07 Å / Origin y: 28.2796 Å / Origin z: 75.8717 Å
111213212223313233
T0.1311 Å2-0.039 Å20.0246 Å2-0.1741 Å20.0128 Å2--0.083 Å2
L0.5126 °2-0.0507 °2-0.3983 °2-0.5968 °2-0.3229 °2--1.8648 °2
S-0.1156 Å °-0.0593 Å °-0.0784 Å °0.0178 Å °0.0527 Å °0.0087 Å °0.3136 Å °-0.3611 Å °0.0562 Å °
Refinement TLS groupSelection details: all

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