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- PDB-4nfh: V207A Horse Liver Alcohol Dehydrogenase E complexed with NAD and ... -

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Basic information

Entry
Database: PDB / ID: 4nfh
TitleV207A Horse Liver Alcohol Dehydrogenase E complexed with NAD and 2,3,4,5,6-pentafluorobenzyl alcohol
ComponentsAlcohol dehydrogenase E chain
KeywordsOXIDOREDUCTASE / Rossmann fold / dehyrogenase / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM) / 2,3,4,5,6-PENTAFLUOROBENZYL ALCOHOL / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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)82,10814
Polymers79,6502
Non-polymers2,45712
Water17,907994
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-20 kcal/mol
Surface area27380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.490, 51.230, 92.320
Angle α, β, γ (deg.)91.96, 103.00, 110.28
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: V207A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Strain: domestic / Plasmid: pBBP/ADHE / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: P00327, alcohol dehydrogenase

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Non-polymers , 5 types, 1006 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-PFB / 2,3,4,5,6-PENTAFLUOROBENZYL ALCOHOL


Mass: 198.090 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H3F5O
#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.: 994 / 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: 48.67 %
Crystal growTemperature: 278 K / Method: microdialysis / pH: 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+, 10 mM 2,3,4,5,6-pentafluorobenzyl alcohol, 12 TO 25 % 2- ...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+, 10 mM 2,3,4,5,6-pentafluorobenzyl alcohol, 12 TO 25 % 2-methyl-2,4-pentanediol, MICRODIALYSIS, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.827 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Dec 13, 2008 / Details: Rosenbaum vertical focussing mirrors
RadiationMonochromator: Rosenbaum-Rock Si(111) sagitally focussed / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.827 Å / Relative weight: 1
ReflectionResolution: 1.2→20 Å / Num. obs: 217807 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.77 % / Biso Wilson estimate: 11.9 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 11.3
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 3.46 % / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 2.4 / Num. unique all: 17131 / % possible all: 74

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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 4DWV

4dwv


Resolution: 1.2→19.84 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.98 / SU B: 1.428 / SU ML: 0.028 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.035 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16569 1066 0.5 %RANDOM
Rwork0.13532 ---
all0.13547 ---
obs0.13547 216747 94.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.966 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å2-0.49 Å20.24 Å2
2--0.23 Å20.15 Å2
3----0.39 Å2
Refine analyzeLuzzati coordinate error free: 0.036 Å
Refinement stepCycle: LAST / Resolution: 1.2→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5566 0 150 994 6710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.026034
X-RAY DIFFRACTIONr_bond_other_d0.0010.025951
X-RAY DIFFRACTIONr_angle_refined_deg1.8922.028196
X-RAY DIFFRACTIONr_angle_other_deg0.911313853
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2445764
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.11424.762210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.387151103
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7011524
X-RAY DIFFRACTIONr_chiral_restr0.110.2971
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216534
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021188
X-RAY DIFFRACTIONr_mcbond_it1.4431.3223024
X-RAY DIFFRACTIONr_mcbond_other1.4431.3223023
X-RAY DIFFRACTIONr_mcangle_it1.6531.9943783
X-RAY DIFFRACTIONr_mcangle_other1.6531.9943784
X-RAY DIFFRACTIONr_scbond_it2.7641.6483010
X-RAY DIFFRACTIONr_scbond_other2.7641.6493011
X-RAY DIFFRACTIONr_scangle_other3.0882.3484406
X-RAY DIFFRACTIONr_long_range_B_refined5.09613.7157809
X-RAY DIFFRACTIONr_long_range_B_other3.81412.0347084
X-RAY DIFFRACTIONr_rigid_bond_restr3.921311985
X-RAY DIFFRACTIONr_sphericity_free41.55410228
X-RAY DIFFRACTIONr_sphericity_bonded10.421012662
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 59 -
Rwork0.293 11932 -
obs-11932 70.35 %

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