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- PDB-1ee2: THE STRUCTURE OF STEROID-ACTIVE ALCOHOL DEHYDROGENASE AT 1.54 A R... -

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Basic information

Entry
Database: PDB / ID: 1ee2
TitleTHE STRUCTURE OF STEROID-ACTIVE ALCOHOL DEHYDROGENASE AT 1.54 A RESOLUTION
ComponentsALCOHOL DEHYDROGENASE
KeywordsOXIDOREDUCTASE / DEHYDROGENASE / ALCOHOL / NICOTINAMIDE COENZYME / STEROID BINDING
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
CHOLIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Alcohol dehydrogenase S chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.54 Å
AuthorsAdolph, H.W.
Citation
Journal: Biochemistry / Year: 2000
Title: Structural basis for substrate specificity differences of horse liver alcohol dehydrogenase isozymes.
Authors: Adolph, H.W. / Zwart, P. / Meijers, R. / Hubatsch, I. / Kiefer, M. / Lamzin, V. / Cedergren-Zeppezauer, E.
#1: Journal: Eur.J.Biochem. / Year: 1991
Title: Substrate Specificity and Stereoselectivity of Horse Liver Alcohol Dehydrogenase. Kinetic Evaluation of Binding and Activation Parameters Controlling the Catalitic Cycles of Unbranched, ...Title: Substrate Specificity and Stereoselectivity of Horse Liver Alcohol Dehydrogenase. Kinetic Evaluation of Binding and Activation Parameters Controlling the Catalitic Cycles of Unbranched, Acyclic Secondary Alcohols and Ketones as Substrates of the Native and Active-Site-Specific Co(II)-Substituted Enzyme
Authors: Adolph, H.W. / Maurer, P. / Scheinder-Bernlohr, H. / Sartorius, C. / Zeppezauer, M.
#2: Journal: J.CHROMATOGR.,A / Year: 1995
Title: Preparation and Characterization of Isozymes and Isoforms of Horse Liver Alcohol Dehydrogenase
Authors: Hubatsch, I. / Maurer, P. / Engel, D. / Adolph, H.W.
#3: 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.
History
DepositionJan 30, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALCOHOL DEHYDROGENASE
B: ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,48810
Polymers79,0822
Non-polymers2,4068
Water18,1951010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
ΔGint-122 kcal/mol
Surface area25880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.030, 73.160, 92.490
Angle α, β, γ (deg.)90.00, 102.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ALCOHOL DEHYDROGENASE


Mass: 39541.090 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / Organ: LIVER / References: UniProt: P00328, 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-CHD / CHOLIC ACID


Mass: 408.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H40O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1010 / 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: 2.3 Å3/Da / Density % sol: 46.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG400, PEG8000, TES/KOH, NAD+, Cholic Acid, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Details: used micro bridge
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14 mg/mlprotein1drop
24 mMNAD+1reservoir
35 mMcholic acid1reservoir
420 %PEG4001reservoircan be replaced by 10% PEG8000
50.1 MTES1reservoircan be replaced by 0.1M KOH, pH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8373
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 23, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8373 Å / Relative weight: 1
ReflectionResolution: 1.54→20 Å / Num. all: 103854 / Num. obs: 103854 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.16 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 10.9
Reflection shellResolution: 1.54→1.57 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.25 / % possible all: 97.2
Reflection
*PLUS
% possible obs: 98.3 %
Reflection shell
*PLUS
% possible obs: 97.2 % / Mean I/σ(I) obs: 4.5

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.54→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Eng & Huber
RfactorNum. reflectionSelection details
Rfree0.183 1000 RANDOM
Rwork0.145 --
all0.148 103584 -
obs0.148 103584 -
Refinement stepCycle: LAST / Resolution: 1.54→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5526 0 150 1010 6686
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.037
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 2 % / Rfactor obs: 0.145
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.04

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