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Basic information

Entry
Database: PDB / ID: 1pl8
Titlehuman SDH/NAD+ complex
Componentshuman sorbitol dehydrogenase
KeywordsOXIDOREDUCTASE / human sorbitol dehydrogenase / NAD
Function / homology
Function and homology information


ribitol 2-dehydrogenase / D-sorbitol dehydrogenase (acceptor) activity / ribitol 2-dehydrogenase activity / L-xylitol catabolic process / L-xylitol metabolic process / (R,R)-butanediol dehydrogenase / (R,R)-butanediol dehydrogenase activity / D-xylulose reductase / sorbitol catabolic process / D-xylulose reductase activity ...ribitol 2-dehydrogenase / D-sorbitol dehydrogenase (acceptor) activity / ribitol 2-dehydrogenase activity / L-xylitol catabolic process / L-xylitol metabolic process / (R,R)-butanediol dehydrogenase / (R,R)-butanediol dehydrogenase activity / D-xylulose reductase / sorbitol catabolic process / D-xylulose reductase activity / L-iditol 2-dehydrogenase / L-iditol 2-dehydrogenase activity / glucuronate catabolic process to xylulose 5-phosphate / Formation of xylulose-5-phosphate / flagellated sperm motility / Fructose biosynthesis / fructose biosynthetic process / motile cilium / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / mitochondrial membrane / glucose metabolic process / NAD binding / carbohydrate binding / extracellular space / extracellular exosome / zinc ion binding / membrane / identical protein binding / cytosol
Similarity search - Function
Sorbitol dehydrogenase-like / 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 ...Sorbitol dehydrogenase-like / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Sorbitol dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPauly, T.A. / Ekstrom, J.L. / Beebe, D.A. / Chrunyk, B. / Cunningham, D. / Griffor, M. / Kamath, A. / Lee, S.E. / Madura, R. / Mcguire, D. ...Pauly, T.A. / Ekstrom, J.L. / Beebe, D.A. / Chrunyk, B. / Cunningham, D. / Griffor, M. / Kamath, A. / Lee, S.E. / Madura, R. / Mcguire, D. / Subashi, T. / Wasilko, D. / Watts, P. / Mylari, B.L. / Oates, P.J. / Adams, P.D. / Rath, V.L.
CitationJournal: Structure / Year: 2003
Title: X-ray crystallographic and kinetic studies of human sorbitol dehydrogenase.
Authors: Pauly, T.A. / Ekstrom, J.L. / Beebe, D.A. / Chrunyk, B. / Cunningham, D. / Griffor, M. / Kamath, A. / Lee, S.E. / Madura, R. / Mcguire, D. / Subashi, T. / Wasilko, D. / Watts, P. / Mylari, B. ...Authors: Pauly, T.A. / Ekstrom, J.L. / Beebe, D.A. / Chrunyk, B. / Cunningham, D. / Griffor, M. / Kamath, A. / Lee, S.E. / Madura, R. / Mcguire, D. / Subashi, T. / Wasilko, D. / Watts, P. / Mylari, B.L. / Oates, P.J. / Adams, P.D. / Rath, V.L.
History
DepositionJun 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _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_asym_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999 The sequence variant Leu -> Gln for residue 238 is noted in Swiss-Prot entry Q00796.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: human sorbitol dehydrogenase
B: human sorbitol dehydrogenase
C: human sorbitol dehydrogenase
D: human sorbitol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,83312
Polymers152,9174
Non-polymers2,9158
Water23,2571291
1
A: human sorbitol dehydrogenase
B: human sorbitol dehydrogenase
hetero molecules

A: human sorbitol dehydrogenase
B: human sorbitol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,83312
Polymers152,9174
Non-polymers2,9158
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_765-x+2,-y+1,z1
Buried area14970 Å2
ΔGint-240 kcal/mol
Surface area50670 Å2
MethodPISA
2
C: human sorbitol dehydrogenase
D: human sorbitol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9166
Polymers76,4592
Non-polymers1,4584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14850 Å2
ΔGint-239 kcal/mol
Surface area50650 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)133.776, 133.776, 224.708
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein
human sorbitol dehydrogenase / / L-iditol 2-dehydrogenase


Mass: 38229.332 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: Q00796, L-iditol 2-dehydrogenase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1291 / 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: 3.79 Å3/Da / Density % sol: 67.57 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.15
Details: NH4AC, NaCitrate, PEG 4000, pH 6.15, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
128 %PEG40001drop
210 mM1dropZnCl2
30.2 mMNAD+1drop
426.5 %PEG40001reservoir
510 mM1reservoirZnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1 Å
DetectorType: BRANDEIS - B1.2 / Detector: CCD / Date: May 18, 2001
Details: double-crystal monochromator Si(111), beam focused by a toroidal mirror
RadiationMonochromator: double-crystal monochromator Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→99 Å / Num. obs: 161025 / % possible obs: 88.6 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 11.8 Å2 / Rsym value: 0.083 / Net I/σ(I): 12.8
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 2 / Num. unique all: 7993 / % possible all: 44.2
Reflection
*PLUS
Highest resolution: 1.9 Å / Redundancy: 4 % / Rmerge(I) obs: 0.083
Reflection shell
*PLUS
% possible obs: 44.2 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→45.82 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 14703 10 %RANDOM
Rwork0.195 ---
all0.195 ---
obs0.195 146788 82.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.2901 Å2 / ksol: 0.401316 e/Å3
Displacement parametersBiso mean: 23.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.62 Å20.85 Å20 Å2
2--2.62 Å20 Å2
3----5.23 Å2
Refine analyzeLuzzati coordinate error free: 0.25 Å / Luzzati sigma a free: 0.24 Å
Refinement stepCycle: LAST / Resolution: 1.9→45.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10708 0 180 1291 12179
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.291 1378 10.1 %
Rwork0.27 12300 -
obs--46.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ALL.PARALL.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 45.8 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.93
LS refinement shell
*PLUS
Rfactor Rwork: 0.27

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