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- PDB-1mgo: Horse Liver Alcohol Dehydrogenase Phe93Ala Mutant -

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Basic information

Entry
Database: PDB / ID: 1mgo
TitleHorse Liver Alcohol Dehydrogenase Phe93Ala Mutant
ComponentsAlcohol Dehydrogenase E chain
KeywordsOXIDOREDUCTASE / Dehydrogenase / Alcohol / Nicotinamide Coenzyme / Mutant / Substrate binding site
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 / 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
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 Angstrom 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 15, 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 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF ONE ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF ONE BIOLOGICALLY ACTIVE DIMERIC MOLECULE AB (2 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,65711
Polymers79,5542
Non-polymers2,1039
Water8,377465
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7130 Å2
ΔGint-133 kcal/mol
Surface area27120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.144, 51.308, 93.481
Angle α, β, γ (deg.)91.98, 103.01, 109.81
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: 39777.180 Da / Num. of mol.: 2 / Mutation: F93A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Gene: M64864 / Plasmid: pBPP / Production host: Escherichia coli (E. coli) / Strain (production host): CJ236 / References: UniProt: P00327, alcohol dehydrogenase

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Non-polymers , 5 types, 474 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.18 %
Crystal growTemperature: 277 K / Method: dialysis / pH: 7 / Details: MPD, pH 7.0, Dialysis, temperature 277K
Crystal grow
*PLUS
Temperature: 253 ℃ / pH: 6.7 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
126 mg/mlenzyme11
213 %MPD12
350 mMammmonium N-[Tris(hydroxymethyl)methyl]-2-aminoethanesulfonate buffer12
40.25 mMEDTA12pH6.7
520 mMNAD+12
6100 mMpentafluorobenzyl alcohol12

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.5418
SYNCHROTRONAPS 17-ID21
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV1IMAGE PLATEJul 25, 2001confocal osmic
MARRESEARCH2CCDNov 11, 2001
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
211
ReflectionResolution: 1.2→20 Å / Num. obs: 199442 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.25 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 5.3
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 1.46 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.29 / % possible all: 84.5
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 86.6 % / Num. measured all: 455785
Reflection shell
*PLUS
% possible obs: 84.5 % / Rmerge(I) obs: 0.29

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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: 1.2→20 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20881 2017 1 %RANDOM
Rwork0.1875 ---
obs0.18772 199422 86.29 %-
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: 17.199 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.72 Å20.18 Å2
2--1.32 Å20.45 Å2
3----1.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.1 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5558 0 92 460 6110
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0225791
X-RAY DIFFRACTIONr_bond_other_d00.025354
X-RAY DIFFRACTIONr_angle_refined_deg1.8431.9967848
X-RAY DIFFRACTIONr_angle_other_deg3.791312531
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1185746
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.120.2913
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026316
X-RAY DIFFRACTIONr_gen_planes_other0.0130.021052
X-RAY DIFFRACTIONr_nbd_refined0.2140.21038
X-RAY DIFFRACTIONr_nbd_other0.1080.25666
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0980.2301
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2650.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1040.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.8131.53704
X-RAY DIFFRACTIONr_mcangle_it2.45425988
X-RAY DIFFRACTIONr_scbond_it3.13832087
X-RAY DIFFRACTIONr_scangle_it4.5514.51860
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.315 133
Rwork0.311 14182
Refinement
*PLUS
Highest resolution: 1.2 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.21 / Rfactor Rwork: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.019
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.84

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