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- PDB-1q1n: APO AND HOLO STRUCTURES OF AN NADP(H)-DEPENDENT CINNAMYL ALCOHOL ... -

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Basic information

Entry
Database: PDB / ID: 1q1n
TitleAPO AND HOLO STRUCTURES OF AN 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 / Oxidoreductases; Acting on NADH or NADPH / cinnamyl-alcohol dehydrogenase activity / alcohol dehydrogenase (NADP+) / alcohol metabolic process / alcohol dehydrogenase (NADP+) activity / cellular aldehyde metabolic process ...hydroxymethylfurfural reductase (NADH) activity / hydroxymethylfurfural reductase (NADPH) activity / furaldehyde metabolic process / 3-methylbutanal reductase (NADPH) activity / Oxidoreductases; Acting on NADH or NADPH / 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-dependent alcohol dehydrogenase 6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.15 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
DepositionJul 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 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)39,8003
Polymers39,6701
Non-polymers1312
Water00
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)79,6016
Polymers79,3392
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Unit cell
Length a, b, c (Å)101.900, 101.900, 149.150
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe biological unit is generated by chain A (x,y,z (1_555), y,x,1-z (4_556)).

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Components

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

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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: 5.64 Å3/Da / Density % sol: 78.17 %
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: BM14 / Wavelength: 1.28197 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 13, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28197 Å / Relative weight: 1
ReflectionResolution: 3.15→30 Å / Num. all: 15485 / Num. obs: 15485 / % possible obs: 96.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
RefinementMethod to determine structure: SAD / Resolution: 3.15→5 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflectionSelection details
Rfree0.283 1117 random
Rwork0.24 --
all0.269 15485 -
obs0.244 11225 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.021 Å2-13.754 Å20 Å2
2---9.021 Å20 Å2
3---18.042 Å2
Refinement stepCycle: LAST / Resolution: 3.15→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2780 0 2 0 2782

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