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- PDB-4dxh: Horse liver alcohol dehydrogenase complexed with NAD+ and 2,2,2-t... -

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Basic information

Entry
Database: PDB / ID: 4dxh
TitleHorse liver alcohol dehydrogenase complexed with NAD+ and 2,2,2-trifluoroethanol
ComponentsAlcohol dehydrogenase E chain
KeywordsOXIDOREDUCTASE / ALCOHOL DEHYDROGENASE / NAD+ / TRIFLUOROETHANOL / MICHAELIS COMPLEX ROSSMANN FOLD
Function / homology
Function and homology information


all-trans-retinol dehydrogenase (NAD+) activity / alcohol dehydrogenase / retinoic acid metabolic process / retinol metabolic process / zinc ion binding / 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 / 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
TRIFLUOROETHANOL / NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM) / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å
AuthorsPlapp, B.V. / Ramaswamy, S.
Citation
Journal: Biochemistry / Year: 2012
Title: Atomic-Resolution Structures of Horse Liver Alcohol Dehydrogenase with NAD(+) and Fluoroalcohols Define Strained Michaelis Complexes.
Authors: Plapp, B.V. / Ramaswamy, S.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Dependence of crystallographic atomic displacement parameters on temperature (25-150 K) for complexes of horse liver alcohol dehydrogenase.
Authors: Plapp, B.V. / Gakhar, L. / Subramanian, R.
#2: Journal: Biochemistry / Year: 2003
Title: Amino acid residues in the nicotinamide binding site contribute to catalysis by horse liver alcohol dehydrogenase.
Authors: Rubach, J.K. / Plapp, B.V.
#3: Journal: J.Biol.Chem. / Year: 2003
Title: Formamides mimic aldehydes and inhibit liver alcohol dehydrogenases and ethanol metabolism.
Authors: Venkataramaiah, T.H. / Plapp, B.V.
History
DepositionFeb 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1May 2, 2012Group: Structure summary
Revision 1.2May 16, 2012Group: Database references
Revision 1.3Jun 27, 2012Group: Database references
Revision 1.4Apr 27, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_related_exp_data_set ...database_2 / pdbx_related_exp_data_set / 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 12, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.6Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alcohol dehydrogenase E chain
B: Alcohol dehydrogenase E chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,96814
Polymers79,7072
Non-polymers2,26112
Water18,4651025
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7450 Å2
ΔGint-112 kcal/mol
Surface area26580 Å2
Unit cell
Length a, b, c (Å)44.250, 51.160, 92.530
Angle α, β, γ (deg.)91.91, 103.02, 109.90
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Alcohol dehydrogenase E chain


Mass: 39853.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Liver / Source: (natural) Equus caballus (horse) / Organ: liver / Strain: Domestic horse / References: UniProt: P00327, alcohol dehydrogenase

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Non-polymers , 5 types, 1037 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NAJ / NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM)


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2
#4: Chemical ChemComp-ETF / TRIFLUOROETHANOL


Mass: 100.040 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3F3O
#5: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1025 / 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: 2.39 Å3/Da / Density % sol: 48.54 %
Crystal growTemperature: 278 K / Method: microdialysis / pH: 6.7
Details: 50 MM AMMONIUM N-[TRIS(HYDROXYMETHYL) METHYL]-2-AMINOETHANE SULFONATE, PH 6.7 (AT 25 C), 0.25 MM EDTA, 10 MG/ML PROTEIN, 1 MM NAD+, 100 MM 2,2,2-TRIFLUOROETHANOL, 12 TO 25 % 2-METHYL-2,4- ...Details: 50 MM AMMONIUM N-[TRIS(HYDROXYMETHYL) METHYL]-2-AMINOETHANE SULFONATE, PH 6.7 (AT 25 C), 0.25 MM EDTA, 10 MG/ML PROTEIN, 1 MM NAD+, 100 MM 2,2,2-TRIFLUOROETHANOL, 12 TO 25 % 2-METHYL-2,4-PENTANEDIOL, TEMPERATURE 278K, MICRODIALYSIS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9184 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2009
Details: Rosenbaum Rock vertical focusing mirror with Pt, glass, Pd lanes
RadiationMonochromator: Rosenbaum Rock high resolution double crystal monochromator, LN2 cooled, sagittal focussing 2nd mirror, Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.12→20 Å / Num. all: 283954 / Num. obs: 267668 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 9.7
Reflection shellResolution: 1.12→1.16 Å / Redundancy: 4 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 2.1 / % possible all: 91.4

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
d*TREKdata reduction
d*TREKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1HLD

1hld


Resolution: 1.12→20 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.979 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 0.94 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14672 1352 0.5 %RANDOM
Rwork0.12653 ---
obs0.12663 266085 94.14 %-
all-283954 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.289 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å2-0.29 Å20.19 Å2
2--0.19 Å20.08 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.12→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5570 0 136 1025 6731
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.026032
X-RAY DIFFRACTIONr_bond_other_d0.0010.024137
X-RAY DIFFRACTIONr_angle_refined_deg1.6362.0248189
X-RAY DIFFRACTIONr_angle_other_deg0.9773.00210268
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1425762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.86924.67212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.191151109
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4471525
X-RAY DIFFRACTIONr_chiral_restr0.140.2975
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216440
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021085
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4581.53780
X-RAY DIFFRACTIONr_mcbond_other0.5021.51544
X-RAY DIFFRACTIONr_mcangle_it2.17926172
X-RAY DIFFRACTIONr_scbond_it3.15532252
X-RAY DIFFRACTIONr_scangle_it4.7984.52010
X-RAY DIFFRACTIONr_rigid_bond_restr2.948310169
X-RAY DIFFRACTIONr_sphericity_free31.44910203
X-RAY DIFFRACTIONr_sphericity_bonded8.9241010907
LS refinement shellResolution: 1.12→1.149 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 93 -
Rwork0.29 19020 -
obs--90.75 %

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