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- PDB-1ps0: Crystal Structure of the NADP(H)-Dependent Cinnamyl Alcohol Dehyd... -

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Basic information

Entry
Database: PDB / ID: 1ps0
TitleCrystal Structure of the NADP(H)-Dependent Cinnamyl Alcohol Dehydrogenase from Saccharomyces cerevisiae
ComponentsHypothetical zinc-type alcohol dehydrogenase-like protein in PRE5-FET4 intergenic region
KeywordsOXIDOREDUCTASE / ADH TOPOLOGY / NADP(H)DEPENDENT
Function / homology
Function and homology information


hydroxymethylfurfural reductase (NADH) activity / hydroxymethylfurfural reductase (NADPH) activity / furaldehyde metabolic process / 3-methylbutanal reductase (NADPH) activity / cinnamyl-alcohol dehydrogenase activity / alcohol dehydrogenase (NADP+) / alcohol metabolic process / alcohol dehydrogenase (NADP+) activity / cellular aldehyde metabolic process / zinc ion binding ...hydroxymethylfurfural reductase (NADH) activity / hydroxymethylfurfural reductase (NADPH) activity / furaldehyde metabolic process / 3-methylbutanal reductase (NADPH) activity / cinnamyl-alcohol dehydrogenase activity / alcohol dehydrogenase (NADP+) / alcohol metabolic process / alcohol dehydrogenase (NADP+) activity / cellular aldehyde metabolic process / zinc ion binding / nucleus / cytoplasm
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 ...: / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NADP-dependent alcohol dehydrogenase 6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsValencia, E. / Larroy, C. / Ochoa, W.F. / Pares, X. / Fita, I. / Biosca, J.A.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Apo and Holo Structures of an NADP(H)-dependent Cinnamyl Alcohol Dehydrogenase from Saccharomyces cerevisiae
Authors: Valencia, E. / Larroy, C. / Ochoa, W.F. / Pares, X. / Fita, I. / Biosca, J.A.
#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
DepositionJun 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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_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_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_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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

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Assembly

Deposited unit
A: Hypothetical zinc-type alcohol dehydrogenase-like protein in PRE5-FET4 intergenic region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5444
Polymers39,6701
Non-polymers8743
Water0
1
A: Hypothetical zinc-type alcohol dehydrogenase-like protein in PRE5-FET4 intergenic region
hetero molecules

A: Hypothetical zinc-type alcohol dehydrogenase-like protein in PRE5-FET4 intergenic region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0878
Polymers79,3392
Non-polymers1,7486
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Unit cell
Length a, b, c (Å)102.132, 102.132, 149.717
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly is a dimer generated by the crystallographic two fold axis: x, y, -z.

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Components

#1: Protein Hypothetical zinc-type alcohol dehydrogenase-like protein in PRE5-FET4 intergenic region / Ciannamyl Alcohol Dehydrogenase


Mass: 39669.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YMR318C (ADH6) / Plasmid: PYES2-YMR318C / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BJ2168 / References: UniProt: Q04894
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3

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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: 5.68 Å3/Da / Density % sol: 78.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2M ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 19, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. all: 18496 / Num. obs: 18395 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.072 / Rsym value: 0.086

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.01→5 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflectionSelection details
Rfree0.298 1327 random
Rwork0.264 --
all0.2978 13635 -
obs0.2676 12308 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--12.842 Å2-14.658 Å20 Å2
2---12.842 Å20 Å2
3---25.684 Å2
Refinement stepCycle: LAST / Resolution: 3.01→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2780 0 50 0 2830
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3nadp_xplor.param

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