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- PDB-1mg0: Horse Liver Alcohol Dehydrogenase Complexed With NAD+ and 2,3-Dif... -

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Basic information

Entry
Database: PDB / ID: 1mg0
TitleHorse Liver Alcohol Dehydrogenase Complexed With NAD+ and 2,3-Difluorobenzyl Alcohol
ComponentsAlcohol Dehydrogenase E chain
KeywordsOXIDOREDUCTASE / dehydrogenase / alcohol / nicotinamide coenzyme / alternative conformation
Function / homology
Function and homology information


all-trans-retinol dehydrogenase (NAD+) activity / alcohol dehydrogenase / alcohol dehydrogenase (NAD+) activity / 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
2,3-DIFLUOROBENZYL ALCOHOL / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRubach, J.K. / Plapp, B.V.
Citation
Journal: Biochemistry / Year: 2002
Title: Mobility of Fluorobenzyl Alcohols Bound to Liver Alcohol Dehydrogenases as Determined by NMR and X-ray Crystallographic Studies
Authors: Rubach, J.K. / 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.
#2: Journal: J.Biol.Chem. / Year: 1982
Title: BINDING OF SUBSTRATE IN A TERNARY COMPLEX OF HORSE LIVER ALCOHOL DEHYDROGENASE
Authors: Eklund, H. / Plapp, B.V. / Samama, J.P. / Branden, C.I.
#3: Journal: J.Mol.Biol. / Year: 1981
Title: STRUCTURE OF A TRICLINIC TERNARY COMPLEX OF HORSE LIVER ALCOHOL DEHYDROGENASE AT 2.9 A RESOLUTION
Authors: Eklund, H. / Samma, J.P. / Wallen, L. / Branden, C.I. / Akeson, A. / Jones, T.A.
#4: Journal: J.Mol.Biol. / Year: 1976
Title: THREE-DIMENSIONAL STRUCTURE OF HORSE LIVER ALCOHOL DEHYDROGENASE AT 2-4 ANGSTROMS RESOLUTION
Authors: Eklund, H. / Nordstrom, B. / Zeppezauer, E. / Soderlund, G. / Ohlsson, I. / Boiwe, T. / Soderberg, B.O. / Tapia, O. / Branden, C.I. / Akeson, A.
History
DepositionAug 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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_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_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
Remark 300BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 OF ...BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 OF THE BIOLOGICALLY ACTIVE DIMERIC MOLECULES AB AND CD (4 CHAINS). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).

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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
C: Alcohol Dehydrogenase E chain
D: Alcohol Dehydrogenase E chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,16720
Polymers159,4134
Non-polymers3,75316
Water16,304905
1
A: Alcohol Dehydrogenase E chain
B: Alcohol Dehydrogenase E chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,58310
Polymers79,7072
Non-polymers1,8778
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-107 kcal/mol
Surface area26610 Å2
MethodPISA
2
C: Alcohol Dehydrogenase E chain
D: Alcohol Dehydrogenase E chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,58310
Polymers79,7072
Non-polymers1,8778
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-110 kcal/mol
Surface area26730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.114, 180.310, 86.912
Angle α, β, γ (deg.)90.00, 105.99, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe enzyme is active as homodimer

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Components

#1: Protein
Alcohol Dehydrogenase E chain


Mass: 39853.273 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / Organ: Liver / References: UniProt: P00327, alcohol dehydrogenase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-DFB / 2,3-DIFLUOROBENZYL ALCOHOL


Mass: 144.119 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H6F2O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 905 / 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: 2.37 Å3/Da / Density % sol: 48.03 %
Crystal growTemperature: 277 K / Method: dialysis / pH: 7 / Details: MPD, pH 7.0, Dialysis, temperature 277K
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 6.7 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
111 %MPD11
250 mMN-[Tris(hydroxymethyl)methyl]-2-aminoethanesulfonate buffer11
30.25 mMEDTA11pH6.7
41 mMNAD+11
517 mM2,3-difluorobenzyl alcohol11
610 mg/mlenzyme12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 12, 2000 / Details: confocal osmic
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 118298 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 16
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.18 / % possible all: 50
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 88 % / Num. measured all: 243387 / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
% possible obs: 50 % / Rmerge(I) obs: 0.18

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Processing

Software
NameVersionClassification
d*TREKdata scaling
d*TREKdata reduction
AMoREphasing
REFMAC5.1.27refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HLD

1hld


Resolution: 1.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21393 1822 1.5 %RANDOM
Rwork0.17916 ---
obs0.17969 118298 88.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.409 Å2
Baniso -1Baniso -2Baniso -3
1-1.82 Å20 Å20.32 Å2
2---1.22 Å20 Å2
3----0.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.132 Å0.144 Å
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11136 0 260 906 12302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02211616
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2881.99515732
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.87551492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0850.21824
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028432
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1920.25658
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.2885
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.6131.57404
X-RAY DIFFRACTIONr_mcangle_it1.133211976
X-RAY DIFFRACTIONr_scbond_it2.06334212
X-RAY DIFFRACTIONr_scangle_it3.45743756
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.313 53
Rwork0.279 4046
Software
*PLUS
Version: 5.1.27 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.214 / Rfactor Rwork: 0.179 / Highest resolution: 1.8 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.012
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.29

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