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- PDB-1pl7: Human Sorbitol Dehydrogenase (apo) -

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Basic information

Entry
Database: PDB / ID: 1pl7
TitleHuman Sorbitol Dehydrogenase (apo)
ComponentsSorbitol dehydrogenase
KeywordsOXIDOREDUCTASE / human sorbitol dehydrogenase
Function / homology
Function and homology information


ribitol 2-dehydrogenase / D-sorbitol dehydrogenase (acceptor) activity / ribitol 2-dehydrogenase (NAD+) activity / xylitol catabolic process / xylitol metabolic process / (R,R)-butanediol dehydrogenase / (R,R)-butanediol dehydrogenase activity / D-xylulose reductase / D-xylulose reductase activity / sorbitol catabolic process ...ribitol 2-dehydrogenase / D-sorbitol dehydrogenase (acceptor) activity / ribitol 2-dehydrogenase (NAD+) activity / xylitol catabolic process / xylitol metabolic process / (R,R)-butanediol dehydrogenase / (R,R)-butanediol dehydrogenase activity / D-xylulose reductase / D-xylulose reductase activity / sorbitol catabolic process / L-iditol 2-dehydrogenase / L-iditol 2-dehydrogenase (NAD+) activity / Formation of xylulose-5-phosphate / D-glucuronate catabolic process to D-xylulose 5-phosphate / Fructose biosynthesis / fructose biosynthetic process / flagellated sperm motility / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / motile cilium / mitochondrial membrane / glucose metabolic process / NAD binding / carbohydrate binding / extracellular space / extracellular exosome / zinc ion binding / identical protein binding / membrane / 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
Sorbitol dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)153,1798
Polymers152,9174
Non-polymers2624
Water20,8431157
1
A: Sorbitol dehydrogenase
B: Sorbitol dehydrogenase
hetero molecules

A: Sorbitol dehydrogenase
B: Sorbitol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,1798
Polymers152,9174
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_765-x+2,-y+1,z1
Buried area10630 Å2
ΔGint-211 kcal/mol
Surface area52200 Å2
MethodPISA
2
C: Sorbitol dehydrogenase
D: Sorbitol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,5894
Polymers76,4592
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10630 Å2
ΔGint-212 kcal/mol
Surface area52200 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)134.946, 134.946, 224.686
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
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1157 / 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: 3.86 Å3/Da / Density % sol: 68.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.15
Details: NH4OAc, NaCitrate, PEG 4000, pH 6.15, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12.0 mg/mlprotein1drop
220 mMHEPES-NaOH1droppH7.8
3100 mM1dropNaCl
42 mMdithiothreitol1drop
50.1 mMNADH1drop
60.2 mMCP-166,5721drop
7150 mM1reservoirNH4OAc
8100 mMsodium citrate1reservoirpH6.15
930 %PEG40001reservoir
102.5 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.979 Å
DetectorType: BRANDEIS - B1.2 / Detector: CCD / Date: Jun 8, 1998
Details: double-crystal monochromator Si(111), beam focused by a toroidal mirror
RadiationMonochromator: double-crystal monochromator Si(111), beam focused by a toroidal mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→99 Å / Num. obs: 125211 / % possible obs: 92.2 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 10.7 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 11.6
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 2 / Num. unique all: 8168 / % possible all: 60.4
Reflection
*PLUS
Lowest resolution: 99 Å / Redundancy: 4 %
Reflection shell
*PLUS
% possible obs: 60.4 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→43.17 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
Rfree0.234 10332 10 %RANDOM
Rwork0.2 ---
all0.2 ---
obs0.2 103565 88.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.1379 Å2 / ksol: 0.369632 e/Å3
Displacement parametersBiso mean: 21.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.98 Å21.31 Å20 Å2
2--1.98 Å20 Å2
3----3.96 Å2
Refine analyzeLuzzati coordinate error free: 0.29 Å / Luzzati sigma a free: 0.26 Å
Refinement stepCycle: LAST / Resolution: 2.2→43.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10708 0 4 1157 11869
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.9
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: 2.2→2.34 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.279 1399 9.9 %
Rwork0.253 12784 -
obs--72.8 %
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: 2.2 Å / Lowest resolution: 43.2 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.233 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9
LS refinement shell
*PLUS
Rfactor Rwork: 0.254

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