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- PDB-3oq6: Horse liver alcohol dehydrogenase A317C mutant complexed with NAD... -

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Basic information

Entry
Database: PDB / ID: 3oq6
TitleHorse liver alcohol dehydrogenase A317C mutant complexed with NAD+ and 2,3,4,5,6-pentafluorobenzyl alcohol
ComponentsAlcohol dehydrogenase E chain
KeywordsOXIDOREDUCTASE / Rossmann fold / alcohol metabolism / NAD
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. / Herdendorf, T.J.
Citation
Journal: Chem.Biol.Interact / Year: 2011
Title: Origins of the high catalytic activity of human alcohol dehydrogenase 4 studied with horse liver A317C alcohol dehydrogenase.
Authors: Herdendorf, T.J. / Plapp, B.V.
#1: Journal: Biochemistry / Year: 1994
Title: Structures of horse liver alcohol dehydrogenase complexed with NAD and substituted benzyl alcohols
Authors: Ramaswamy, S. / Eklund, H. / Plapp, B.V.
History
DepositionSep 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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)82,11013
Polymers79,7712
Non-polymers2,33911
Water19,7801098
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7460 Å2
ΔGint-111 kcal/mol
Surface area26610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.340, 51.310, 92.210
Angle α, β, γ (deg.)91.980, 102.950, 110.110
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: 39885.336 Da / Num. of mol.: 2 / Mutation: A317C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Gene: ADH E / Plasmid: pET23d(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(lamdaDE3) / References: UniProt: P00327, alcohol dehydrogenase

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Non-polymers , 5 types, 1109 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.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1098 / 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: 48.51 %
Crystal growTemperature: 298 K / Method: microdialysis / pH: 7
Details: 50 mM ammonium TES [N-tris(hydroxymethyl)-2-aminoethane sulfonate], 25% MRD, 11 mg/ml protein, 11 mM NAD+, 5 mM 2,3,4,5,6-pentafluorobenzyl alcohol, pH 7.0, MICRODIALYSIS, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.8 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Mar 27, 2009 / Details: SAGGITALLY FOCUSED MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.2→90 Å / Num. obs: 214213 / % possible obs: 92.2 % / Redundancy: 3.57 % / Biso Wilson estimate: 11.5 Å2 / Rmerge(I) obs: 0.061 / Χ2: 1 / Net I/σ(I): 9.4 / Scaling rejects: 5787
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.2-1.243.430.28136677519347183.6
1.24-1.293.550.2593.372278203100.9687.2
1.29-1.353.520.2423.672495205611.0188.4
1.35-1.423.510.2144.17303820802189.6
1.42-1.513.470.18573901212521.0191.4
1.51-1.633.460.1366.774762215430.9892.8
1.63-1.793.50.0939.577971221470.9495.2
1.79-2.053.680.07811.883709225990.9697.3
2.05-2.583.780.0616.487014227460.9398.1
2.58-19.853.790.04525.689516229061.1698.5

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Processing

Software
NameVersionClassificationNB
d*TREK9.9.1LDzdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1hld

1hld


Resolution: 1.2→19.85 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.977 / WRfactor Rfree: 0.1748 / WRfactor Rwork: 0.1442 / Occupancy max: 1 / Occupancy min: 0.03 / FOM work R set: 0.8668 / SU B: 1.303 / SU ML: 0.026 / SU R Cruickshank DPI: 0.0359 / SU Rfree: 0.0362 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY. B107 GLU O TOO CLOSE TO B741 O, BECAUSE OF A WOBBLE IN THE PEPTIDE BACKBONE THAT THE AUTHORS ARE UNABLE TO FIT PROPERLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1621 1061 50 %RANDOM
Rwork0.135 ---
obs0.1351 214172 92.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 97.31 Å2 / Biso mean: 17.5778 Å2 / Biso min: 5.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0.31 Å20.41 Å2
2---0.32 Å20.12 Å2
3---0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.2→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5572 0 142 1098 6812
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225983
X-RAY DIFFRACTIONr_bond_other_d0.0010.024090
X-RAY DIFFRACTIONr_angle_refined_deg1.6162.0268116
X-RAY DIFFRACTIONr_angle_other_deg0.9893.00210137
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1825754
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.98124.686207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.074151085
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8941524
X-RAY DIFFRACTIONr_chiral_restr0.0960.2955
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216394
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021066
X-RAY DIFFRACTIONr_mcbond_it1.5811.53748
X-RAY DIFFRACTIONr_mcbond_other0.841.51534
X-RAY DIFFRACTIONr_mcangle_it2.34426121
X-RAY DIFFRACTIONr_scbond_it3.34332235
X-RAY DIFFRACTIONr_scangle_it4.9594.51991
X-RAY DIFFRACTIONr_rigid_bond_restr1.331310073
LS refinement shellResolution: 1.2→1.229 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.203 69 -
Rwork0.223 14103 -
all-14172 -
obs--83.72 %

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