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- PDB-4nfs: V203A horse liver alcohol dehydrogenase E complexed with NAD and ... -

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Basic information

Entry
Database: PDB / ID: 4nfs
TitleV203A horse liver alcohol dehydrogenase E complexed with NAD and 2,2,2-trifluoroethanol
ComponentsAlcohol dehydrogenase E chain
KeywordsOXIDOREDUCTASE / Rossmann fold / dehydrogenase / NAD / liver cytosol
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: 1.1 Å
AuthorsPlapp, B.V.
CitationJournal: Biochemistry / Year: 2014
Title: Effects of cavities at the nicotinamide binding site of liver alcohol dehydrogenase on structure, dynamics and catalysis.
Authors: Yahashiri, A. / Rubach, J.K. / Plapp, B.V.
History
DepositionOct 31, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _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_ref_seq_dif.details / _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: Alcohol dehydrogenase E chain
B: Alcohol dehydrogenase E chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,91214
Polymers79,6502
Non-polymers2,26112
Water18,6281034
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7510 Å2
ΔGint-112 kcal/mol
Surface area26550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.280, 51.410, 92.530
Angle α, β, γ (deg.)91.88, 103.09, 109.94
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: 39825.223 Da / Num. of mol.: 2 / Mutation: V203A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Strain: domestic horse / Plasmid: pBBP/EqADH E / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: P00327, alcohol dehydrogenase

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Non-polymers , 5 types, 1046 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.: 1034 / 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: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 278 K / Method: microdialysis / pH: 7
Details: 50 mN ammonium N-[tris(hydroxymethyl)methyl]-2-amminoethanesulfonate and 0.5 mM EDTA, pH 6.7 (at 25 deg C), 10 mg/ml protein, 1 mM NAD+, 100 mM 2,2,2-trifluoroethanol, 13-25 % 2-methyl-2,4- ...Details: 50 mN ammonium N-[tris(hydroxymethyl)methyl]-2-amminoethanesulfonate and 0.5 mM EDTA, pH 6.7 (at 25 deg C), 10 mg/ml protein, 1 mM NAD+, 100 mM 2,2,2-trifluoroethanol, 13-25 % 2-methyl-2,4-methylpentanediol, MICRODIALYSIS, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.802 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jul 13, 2007 / Details: Rosenbaum-Rock vertically focussed mirrors
RadiationMonochromator: Rosenbaum-Rock Si(111) sagitally focussed / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.802 Å / Relative weight: 1
ReflectionResolution: 1.1→20 Å / Num. all: 310308 / Num. obs: 266123 / % possible obs: 88.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.05 % / Biso Wilson estimate: 11.9 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 12.2
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 2.91 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 2.2 / Num. unique all: 15266 / % possible all: 50.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
REFMAC5.7.0032refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4DXH

4dxh


Resolution: 1.1→19.58 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.052 / SU ML: 0.022 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17474 2690 1 %RANDOM
Rwork0.13743 ---
obs0.13781 263388 88.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.884 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0.08 Å2-0.02 Å2
2--0.21 Å2-0.34 Å2
3----0.16 Å2
Refine analyzeLuzzati coordinate error free: 0.033 Å
Refinement stepCycle: LAST / Resolution: 1.1→19.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5566 0 136 1034 6736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.026079
X-RAY DIFFRACTIONr_bond_other_d0.0020.026025
X-RAY DIFFRACTIONr_angle_refined_deg1.9332.0168255
X-RAY DIFFRACTIONr_angle_other_deg0.927314018
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2565770
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.07124.558215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.105151120
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3551527
X-RAY DIFFRACTIONr_chiral_restr0.1210.2980
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216582
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021209
X-RAY DIFFRACTIONr_mcbond_it1.6571.3893041
X-RAY DIFFRACTIONr_mcbond_other1.6571.3893040
X-RAY DIFFRACTIONr_mcangle_it1.7552.0943811
X-RAY DIFFRACTIONr_mcangle_other1.7552.0943812
X-RAY DIFFRACTIONr_scbond_it3.171.7393038
X-RAY DIFFRACTIONr_scbond_other3.1711.743039
X-RAY DIFFRACTIONr_scangle_other3.3382.484439
X-RAY DIFFRACTIONr_long_range_B_refined5.86814.4197917
X-RAY DIFFRACTIONr_long_range_B_other4.21812.617156
X-RAY DIFFRACTIONr_rigid_bond_restr12.098312104
X-RAY DIFFRACTIONr_sphericity_free53.32210236
X-RAY DIFFRACTIONr_sphericity_bonded13.9321012813
LS refinement shellResolution: 1.1→1.128 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 109 -
Rwork0.345 10674 -
obs--48.44 %

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