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- PDB-1e3j: Ketose reductase (sorbitol dehydrogenase) from silverleaf whitefly -

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Basic information

Entry
Database: PDB / ID: 1e3j
TitleKetose reductase (sorbitol dehydrogenase) from silverleaf whitefly
ComponentsNADP(H)-DEPENDENT KETOSE REDUCTASE
KeywordsOXIDOREDUCTASE / FRUCTOSE REDUCTION
Function / homology
Function and homology information


sorbitol catabolic process / L-iditol 2-dehydrogenase (NAD+) activity / zinc ion binding
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
BORIC ACID / PHOSPHATE ION / Sorbitol dehydrogenase
Similarity search - Component
Biological speciesBEMISIA ARGENTIFOLII (silverleaf whitefly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsBanfield, M.J. / Salvucci, M.E. / Baker, E.N. / Smith, C.A.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Crystal Structure of Nadp(H)-Dependent Ketose Reductase from Besimia Argentifolii at 2.3 Angstrom Resolution
Authors: Banfield, M.J. / Salvucci, M.E. / Baker, E.N. / Smith, C.A.
#1: Journal: J.Mol.Biol. / Year: 1998
Title: Nadp-Dependent Bacterial Alcohol Dehydrogenases: Crystal Structure, Co-Factor-Binding and Co-Factor Specificity of the Adhs of Clostridium Beijerinckii and Thermoanaerobacter Brockii
Authors: Korkhin, Y. / Kalb, A.J. / Peretz, M. / Bogin, O. / Burstein, Y. / Frolow, F.
#2: Journal: J.Mol.Biol. / Year: 1976
Title: Nadp-Dependent Bacterial Alcohol Dehydrogenases: Crystal Structure, Co-Factor-Binding and Co-Factor Specificity of the Adhs of Clostridium Beijerinckii and Thermoanaerobacter Brockii
Authors: Eklund, H. / Nordstrom, B. / Zeppezauer, E. / Soderlund, G. / Ohlsson, I. / Boiwe, T. / Soderberg, B.O. / Tapia, O. / Branden, C.I.
History
DepositionJun 19, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 4, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_conn.ptnr2_label_seq_id / _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: NADP(H)-DEPENDENT KETOSE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5015
Polymers38,2131
Non-polymers2884
Water84747
1
A: NADP(H)-DEPENDENT KETOSE REDUCTASE
hetero molecules

A: NADP(H)-DEPENDENT KETOSE REDUCTASE
hetero molecules

A: NADP(H)-DEPENDENT KETOSE REDUCTASE
hetero molecules

A: NADP(H)-DEPENDENT KETOSE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,00320
Polymers152,8534
Non-polymers1,15016
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
crystal symmetry operation3_756-x+2,y,-z+11
crystal symmetry operation2_755-x+2,-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)78.822, 98.395, 120.924
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-2013-

HOH

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Components

#1: Protein NADP(H)-DEPENDENT KETOSE REDUCTASE


Mass: 38213.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BEMISIA ARGENTIFOLII (silverleaf whitefly)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O96496
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-BO3 / BORIC ACID


Mass: 61.833 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BH3O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 3.06 Å3/Da / Density % sol: 53.3 %
Crystal growpH: 8.75
Details: 1.4M AMMONIUM SUPLHATE, 6% (V/V) GLYCERO 100MM BORIC ACID, PH8.75
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
21.4 Mammonium sulfate1reservoir
36 %glycerol1reservoir
40.1 Mboric acid1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9998, 1.1807, 1.2825, 1.2829
DetectorType: ADSC QUANTUM / Detector: CCD / Date: Feb 15, 2000 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.99981
21.18071
31.28251
41.28291
ReflectionResolution: 2.3→22 Å / Num. obs: 21214 / % possible obs: 97.5 % / Redundancy: 13.3 % / Biso Wilson estimate: 41.1 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 44.9
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.205 / Mean I/σ(I) obs: 7.9 / % possible all: 95.5
Reflection
*PLUS
Lowest resolution: 22 Å
Reflection shell
*PLUS
% possible obs: 95.5 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS1phasing
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.3→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2766186.47 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE C-TERMINAL RESIDUE WAS NOT SEEN I THE DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1074 5.2 %RANDOM
Rwork0.219 ---
obs0.219 20818 98 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.7918 Å2 / ksol: 0.314832 e/Å3
Displacement parametersBiso mean: 49.5 Å2
Baniso -1Baniso -2Baniso -3
1-8.87 Å20 Å20 Å2
2---6.01 Å20 Å2
3----2.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2568 0 11 47 2626
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
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_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.14
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: 2.3→2.44 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.343 157 4.5 %
Rwork0.267 3324 -
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.14
LS refinement shell
*PLUS
Lowest resolution: 2.38 Å / Rfactor Rfree: 0.345 / Rfactor obs: 0.27

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