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- PDB-1e3e: Mouse class II alcohol dehydrogenase complex with NADH -

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Basic information

Entry
Database: PDB / ID: 1e3e
TitleMouse class II alcohol dehydrogenase complex with NADH
ComponentsALCOHOL DEHYDROGENASE, CLASS II
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


Ethanol oxidation / alcohol catabolic process / quinone metabolic process / ethanol metabolic process / RA biosynthesis pathway / all-trans-retinol dehydrogenase (NAD+) / all-trans retinal binding / fatty acid omega-oxidation / quinone reductase (NADPH) activity / benzaldehyde dehydrogenase (NAD+) activity ...Ethanol oxidation / alcohol catabolic process / quinone metabolic process / ethanol metabolic process / RA biosynthesis pathway / all-trans-retinol dehydrogenase (NAD+) / all-trans retinal binding / fatty acid omega-oxidation / quinone reductase (NADPH) activity / benzaldehyde dehydrogenase (NAD+) activity / aldehyde metabolic process / alcohol dehydrogenase (NAD+) activity / all-trans-retinol dehydrogenase (NAD+) activity / aldose reductase (NADPH) activity / retinol metabolic process / retinol binding / NAD binding / zinc ion binding / nucleoplasm / cytosol
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 / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain ...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 / 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
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / All-trans-retinol dehydrogenase [NAD(+)] ADH4
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsSvensson, S. / Hoeoeg, J.O. / Schneider, G. / Sandalova, T.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Crystal Structure of Mouse Class II Alcohol Dehydrogenase Reveal Determinants of Substrate Specificity and Catalytic Efficiency
Authors: Svensson, S. / Hoeoeg, J.O. / Schneider, G. / Sandalova, T.
#1: Journal: J.Biol.Chem. / Year: 1999
Title: A Novel Subtype of Class II Alcohol Dehydrogenase in Rodents
Authors: Svensson, S. / Stroemberg, P. / Hoeoeg, J.O.
History
DepositionJun 14, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 12, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Jan 17, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_residues / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / 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.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

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Assembly

Deposited unit
A: ALCOHOL DEHYDROGENASE, CLASS II
B: ALCOHOL DEHYDROGENASE, CLASS II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7818
Polymers80,1892
Non-polymers1,5936
Water9,044502
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-121.3 kcal/mol
Surface area29210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.275, 82.900, 105.528
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ALCOHOL DEHYDROGENASE, CLASS II


Mass: 40094.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Gene: ADH-2 / Organ: LIVER / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9QYY9, alcohol dehydrogenase
#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / 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: 2.06 Å3/Da / Density % sol: 39.3 %
Crystal growpH: 8.3 / Details: pH 8.30
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MBicine1reservoir
21 mMNADH1reservoir
314.0 %(w/w)PEG60001reservoir
411 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.015
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.015 Å / Relative weight: 1
ReflectionResolution: 2.12→25 Å / Num. obs: 39383 / % possible obs: 92.9 % / Redundancy: 5.8 % / Biso Wilson estimate: 26.34 Å2 / Rsym value: 0.062 / Net I/σ(I): 19.5
Reflection shellResolution: 2.08→2.15 Å / Rsym value: 0.164 / % possible all: 57.3
Reflection
*PLUS
Num. measured all: 231825 / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 59.4 % / Rmerge(I) obs: 0.164 / Mean I/σ(I) obs: 11.1

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CDO

1cdo


Resolution: 2.12→25 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1980 4.7 %RANDOM
Rwork0.202 ---
obs0.202 38896 94.7 %-
Solvent computationSolvent model: ANISOTROPIC BULK SOLVENT CORRECTION
Displacement parametersBiso mean: 31.35 Å2
Baniso -1Baniso -2Baniso -3
1-7.402 Å20 Å20 Å2
2---12.903 Å20 Å2
3---5.508 Å2
Refine analyzeLuzzati d res low obs: 25 Å
Refinement stepCycle: LAST / Resolution: 2.12→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5578 0 92 502 6172
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0079
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_deg1.316
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
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: 2.12→2.14 Å / Total num. of bins used: 38
RfactorNum. reflection% reflection
Rfree0.3626 29 5 %
Rwork0.2729 544 -
obs--51 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:WATER_REP.PARAM
X-RAY DIFFRACTION2CNS_TOPPAR:ION.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.259
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.263

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