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- PDB-1het: atomic X-ray structure of liver alcohol dehydrogenase containing ... -

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Basic information

Entry
Database: PDB / ID: 1het
Titleatomic X-ray structure of liver alcohol dehydrogenase containing a hydroxide adduct to NADH
ComponentsALCOHOL DEHYDROGENASE E CHAIN
KeywordsOXIDOREDUCTASE / OXIDOREDUCTASE(NAD(A)-CHOH(D))
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 / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEQUUS CABALLUS (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsMeijers, R. / Morris, R.J. / Adolph, H.W. / Merli, A. / Lamzin, V.S. / Cedergen-Zeppezauer, E.S.
Citation
#1: Journal: Biochemistry / Year: 1999
Title: Substitutions in a Flexible Loop of Horse Liver Alcohol Dehydrogenase Hinder the Conformational Change and Unmask Hydrogen Transfer
Authors: Ramaswamy, S. / Park, D.H. / Plapp, B.V.
#2: Journal: Biochemistry / Year: 1997
Title: Electrostatic Effects in the Kinetics of Coenzyme Binding to Isozymes of Alcohol Dehydrogenase from Horse Liver
Authors: Adolph, H.W. / Kiefer, M. / Cedergren-Zeppezauer, E.S.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Refined Structure of Cu-Substituted Alcohol Dehydrogenase at 2.1 A Resolution
Authors: Al-Karadaghi, S. / Cedergren-Zeppezauer, E.S. / Dauter, Z. / Wilson, K.S.
#4: Journal: Acta Crystallogr.,Sect.D / Year: 1994
Title: Refined Crystal Structure of Liver Alcohol Dehydrogenase-Nadh Complex at 1.8 Angstrom Resolution
Authors: Al-Karadaghi, S. / Cedergren-Zeppezauer, E.S. / Petratos, K. / Hovmoeller, S. / Terry, H. / Dauter, Z. / Wilson, K.S.
#5: Journal: J.Biol.Chem. / Year: 1986
Title: Interdomain Motion in Liver Alcohol Dehydrogenase. {S}Tructural and Energetic Analysis of the Hinge Bending Mode
Authors: Colonna-Cesari, F. / Perahia, D. / Karplus, M. / Eklund, H. / Branden, C.I. / Tapia, O.
#6: Journal: Biochemistry / Year: 1984
Title: Crystallographic Investigations of Nicotinamide Adenine Dinucleotide
Authors: Eklund, H. / Samama, J.-P. / Jones, T.A.
#7: Journal: Proc.Natl.Acad.Sci.USA / Year: 1983
Title: Crystal Structures of the Active Site in Specifically Metal-Depleted and Cobalt-Substituted Horse Liver Alcohol Dehydrogenase Derivatives
Authors: Schneider, G. / Eklund, H. / Cedergren-Zeppezauer, E. / Zeppezauer, M.
#8: Journal: Biochemistry / Year: 1983
Title: Crystal-Structure Determination of Reduced Nicotinamide Adenine Dinucleotide Complex with Horse Liver Alcohol Dehydrogenase Maintained in its Apo Conformation by Zinc-Bound Imidazole
Authors: Cedergren-Zeppezauer, E.
#9: Journal: Biochemistry / Year: 1982
Title: Crystal Structure Determinations of Coenzyme Analogue and Substrate Complexes of Liver Alcohol Dehydrogenase: Binding of 1,4,5,6-Tetrahydronicotinamide Adenine Dinucleotide and Trans-4- ...Title: Crystal Structure Determinations of Coenzyme Analogue and Substrate Complexes of Liver Alcohol Dehydrogenase: Binding of 1,4,5,6-Tetrahydronicotinamide Adenine Dinucleotide and Trans-4-({N},{N}-Dimethylamino)Cinnamaldehyde to the Enzyme
Authors: Cedergren-Zeppezauer, E. / Samama, J.-P. / Eklund, H.
#10: Journal: J.Mol.Biol. / Year: 1976
Title: Three-Dimensional Structure of Horse Liver Alcohol Dehydrogenase at 2.4 Angstrom Resolution
Authors: Eklund, H. / Nordstrom, B. / Zeppezauer, E. / Soderlund, G. / Ohlsson, I. / Boiwe, T. / Soderberg, B.-O. / Tapia, O. / Branden, C.-I. / Akeson, A.
#11: Journal: Proc.Natl.Acad.Sci.USA / Year: 1973
Title: Structure of Liver Alcohol Dehydrogenase at 2.9 Angstrom Resolution
Authors: Branden, C.-I. / Eklund, H. / Nordstrom, B. / Boiwe, T. / Soderlund, G. / Zeppezauer, E. / Ohlsson, I. / Akeson, A.
History
DepositionNov 25, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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.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_ptnr2_label_alt_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_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 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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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)81,65011
Polymers79,7072
Non-polymers1,9439
Water25,8701436
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-28.2 kcal/mol
Surface area32800 Å2
MethodPQS
Unit cell
Length a, b, c (Å)51.100, 44.400, 94.000
Angle α, β, γ (deg.)104.60, 101.50, 70.50
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.12925, 0.98584, -0.10681), (0.98615, -0.13908, -0.09037), (-0.10394, -0.09366, -0.99016)
Vector: 0.399, -0.2149, 0.4423)
DetailsBIOLOGICAL_UNIT: DIMERIC

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Components

#1: Protein ALCOHOL DEHYDROGENASE E CHAIN / ALCOHOL DEHYDROGENASE I


Mass: 39853.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: ADDUCT BETWEEN NC6 OF NADH AND ZINC BOUND HYDROXIDE
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.: 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-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1436 / Source method: isolated from a natural source / Formula: H2O
Compound detailsALCOHOL + NAD(+) = ALDEHYDE OR KETONE + NADH. REQUIRES ZINC FOR ITS ACTIVITY. DIMER OF IDENTICAL OR ...ALCOHOL + NAD(+) = ALDEHYDE OR KETONE + NADH. REQUIRES ZINC FOR ITS ACTIVITY. DIMER OF IDENTICAL OR NONIDENTICAL CHAINS OF TWO TYPES (E AND S) CODED BY 2 SEPARATE GENES AT DIFFERENT LOCI.

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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: 2.42 Å3/Da / Density % sol: 49.2 %
Crystal growpH: 8.2 / Details: pH 8.20
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %PEG40011
20.05 MTris-HCl11
30.5 %MPD11

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.927
DetectorType: MARRESEARCH X-RAY RESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.927 Å / Relative weight: 1
ReflectionResolution: 1.1→20 Å / Num. obs: 267243 / % possible obs: 94.5 % / Redundancy: 2.6 % / Biso Wilson estimate: 9.4 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 13.1
Reflection shellResolution: 1.1→1.12 Å / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2 / % possible all: 89.7
Reflection
*PLUS
Num. measured all: 684025

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OHX

2ohx


Resolution: 1.15→20 Å / Cross valid method: THROUGHOUT UNTIL FINAL REFINEMENT ROUND / σ(F): 0 / ESU R: 0.03
Details: SHELX WAS USED IN PARALLEL TO REFINE OCCUPANCIES OF DISORDERED RESIDUES
RfactorNum. reflection% reflectionSelection details
Rfree0.135 -0.05 %RANDOM
Rwork0.118 ---
obs0.123 252601 94.5 %-
Displacement parametersBiso mean: 19.8 Å2
Refinement stepCycle: LAST / Resolution: 1.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5570 0 116 1436 7122
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.015
X-RAY DIFFRACTIONp_angle_d0.034
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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