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- PDB-3bto: HORSE LIVER ALCOHOL DEHYDROGENASE COMPLEXED TO NADH AND (1S,3S)3-... -

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Basic information

Entry
Database: PDB / ID: 3bto
TitleHORSE LIVER ALCOHOL DEHYDROGENASE COMPLEXED TO NADH AND (1S,3S)3-BUTYLTHIOLANE 1-OXIDE
ComponentsLIVER ALCOHOL DEHYDROGENASE
KeywordsOXIDOREDUCTASE / DEHYDROGENASE / ALCOHOL / NICOTINAMIDE COENZYME / SULFOXIDE
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 / 3-BUTYLTHIOLANE 1-OXIDE / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsRamaswamy, S. / Plapp, B.V.
Citation
Journal: Biochemistry / Year: 1997
Title: Flexibility of liver alcohol dehydrogenase in stereoselective binding of 3-butylthiolane 1-oxides.
Authors: Cho, H. / Ramaswamy, S. / Plapp, B.V.
#1: 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.
#2: 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.
#3: Journal: J.Mol.Biol. / Year: 1976
Title: Three-Dimensional Structure of Horse Liver Alcohol Dehydrogenase at 2.4 A 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
DepositionNov 8, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LIVER ALCOHOL DEHYDROGENASE
B: LIVER ALCOHOL DEHYDROGENASE
C: LIVER ALCOHOL DEHYDROGENASE
D: LIVER ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,23120
Polymers159,4134
Non-polymers3,81816
Water29,0941615
1
A: LIVER ALCOHOL DEHYDROGENASE
D: LIVER ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,61610
Polymers79,7072
Non-polymers1,9098
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7090 Å2
ΔGint-113 kcal/mol
Surface area26380 Å2
MethodPISA
2
B: LIVER ALCOHOL DEHYDROGENASE
C: LIVER ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,61610
Polymers79,7072
Non-polymers1,9098
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7070 Å2
ΔGint-109 kcal/mol
Surface area26360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.930, 180.200, 86.800
Angle α, β, γ (deg.)90.00, 106.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.99595, 0.00937, -0.08941), (-0.00759, 0.99977, 0.02027), (0.08958, -0.01951, 0.99579)14.41609, -0.16016, 39.98553
2given(0.07702, -0.128, 0.98878), (-0.10109, -0.98762, -0.11997), (0.99189, -0.09072, -0.08901)19.8501, 44.20871, 39.25481
3given(0.17142, -0.11699, 0.97823), (-0.1089, -0.98909, -0.0992), (0.97916, -0.08953, -0.18229)4.73266, 44.09769, -0.32316

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Components

#1: Protein
LIVER ALCOHOL DEHYDROGENASE / ADH


Mass: 39853.273 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: COMMERCIAL PREPARATION OF ENZYME FROM HORSE LIVER. CDNA SEQUENCE M64864
Source: (natural) Equus caballus (horse) / Cellular location: CYTOPLASM / 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-SSB / 3-BUTYLTHIOLANE 1-OXIDE


Mass: 160.277 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H16OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1615 / 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: 2.35 Å3/Da / Density % sol: 47 %
Crystal growMethod: batch dialysis / pH: 7
Details: PROTEIN WAS CRYSTALLIZED BY THE BATCH DIALYSIS METHOD USING MPD AS THE PRECIPITANT AT PH 7.0, 50 MM AMMONIUM N-[TRIS(HYDROXYMETHYL)METHYL]-2 AMINOETHANESULFONATE, WITH 0.66 MM NADH AND 0.76 ...Details: PROTEIN WAS CRYSTALLIZED BY THE BATCH DIALYSIS METHOD USING MPD AS THE PRECIPITANT AT PH 7.0, 50 MM AMMONIUM N-[TRIS(HYDROXYMETHYL)METHYL]-2 AMINOETHANESULFONATE, WITH 0.66 MM NADH AND 0.76 MM 3-BUTYLTHIOLANE 1-OXIDE., batch dialysis
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlenzyme11
250 mMammonium N-[tris(hydroxymethyl)methyl]-2-aminoethanesulfonate12
30.66 mMNADH12
40.23 mMP112or 0.76 mM P3
525 %MPD12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.99
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.66→20 Å / Num. obs: 155052 / % possible obs: 89.8 % / Redundancy: 2 % / Biso Wilson estimate: 13.96 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.061 / Net I/σ(I): 12.6
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 2 % / Rmerge(I) obs: 0.135 / Mean I/σ(I) obs: 5.6 / Rsym value: 0.138 / % possible all: 73.6
Reflection
*PLUS
Num. measured all: 307946
Reflection shell
*PLUS
% possible obs: 73.6 %

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HLD

1hld


Resolution: 1.66→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1552 1 %RANDOM
Rwork0.185 ---
obs0.207 155052 89.8 %-
Displacement parametersBiso mean: 15.3 Å2
Refinement stepCycle: LAST / Resolution: 1.66→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11140 0 224 1543 12907
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.02
X-RAY DIFFRACTIONp_angle_d0.030.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.040.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.512
X-RAY DIFFRACTIONp_mcangle_it1.993
X-RAY DIFFRACTIONp_scbond_it2.052
X-RAY DIFFRACTIONp_scangle_it33
X-RAY DIFFRACTIONp_plane_restr0.03
X-RAY DIFFRACTIONp_chiral_restr0.1430.15
X-RAY DIFFRACTIONp_singtor_nbd0.1760.3
X-RAY DIFFRACTIONp_multtor_nbd0.2630.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor5.47
X-RAY DIFFRACTIONp_staggered_tor13.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor33.120
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.181 / Rfactor Rfree: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS

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