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- PDB-1p0c: Crystal Structure of the NADP(H)-Dependent Vertebrate Alcohol Deh... -

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Basic information

Entry
Database: PDB / ID: 1p0c
TitleCrystal Structure of the NADP(H)-Dependent Vertebrate Alcohol Dehydrogenase (ADH8)
ComponentsNADP-dependent ALCOHOL DEHYDROGENASE
KeywordsOXIDOREDUCTASE / ADH TOPOLOGY / NADP(H)-DEPENDENT
Function / homology
Function and homology information


alcohol dehydrogenase (NADP+) / alcohol dehydrogenase (NADP+) activity / all-trans-retinol 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 / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain ...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 / 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
PHOSPHATE ION / NADP-dependent alcohol dehydrogenase
Similarity search - Component
Biological speciesRana perezi (Iberian green frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRosell, A. / Valencia, E. / Pares, X. / Fita, I. / Farres, J. / Ochoa, W.F.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Crystal Structure of the Vertebrate NADP(H)-dependent Alcohol Dehydrogenase (ADH8)
Authors: Rosell, A. / Valencia, E. / Pares, X. / Fita, I. / Farres, J. / Ochoa, W.F.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Crystallization and preliminary X-ray analysis of NADP(H)-dependent alcohol dehydrogenases from Saccharomyces cerevisiae and Rana perezi
Authors: Valencia, E. / Rosell, A. / Larroy, C. / Farres, J. / Biosca, J.A. / Fita, I. / Pares, X. / Ochoa, W.F.
History
DepositionApr 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: NADP-dependent ALCOHOL DEHYDROGENASE
B: NADP-dependent ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,12310
Polymers78,4872
Non-polymers6368
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-109 kcal/mol
Surface area28000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.551, 79.523, 91.892
Angle α, β, γ (deg.)90.00, 113.10, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein NADP-dependent ALCOHOL DEHYDROGENASE


Mass: 39243.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rana perezi (Iberian green frog) / Gene: ADH / Plasmid: pGEX4T-2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O57380, alcohol dehydrogenase (NADP+)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.54 Å3/Da / Density % sol: 51.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 4000, LiSO4, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal grow
*PLUS
Temperature: 293 K
Details: Valencia, E., (2003) Acta Crystallogr., Sect.D, 59, 334.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 mg/mlprotein1drop
22 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.953 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 8, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 79197 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection
*PLUS
Num. measured all: 150436 / Rmerge(I) obs: 0.113
Reflection shell
*PLUS
Highest resolution: 2.1 Å / % possible obs: 99 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.234 169 -random
Rwork0.198 ---
obs-40879 52.6 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.497 Å20 Å2-3.914 Å2
2---5.981 Å20 Å2
3---6.478 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5456 0 26 307 5789
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it1.3011.5
X-RAY DIFFRACTIONo_mcangle_it2.052
X-RAY DIFFRACTIONo_scbond_it2.3522
X-RAY DIFFRACTIONo_scangle_it3.322.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4cry.param
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.005
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.31

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