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- PDB-1y1p: X-ray structure of aldehyde reductase with NADPH -

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Basic information

Entry
Database: PDB / ID: 1y1p
TitleX-ray structure of aldehyde reductase with NADPH
ComponentsAldehyde reductase IIAldose reductase
KeywordsOXIDOREDUCTASE / Rossmann fold / short chain dehydrogenase reductase
Function / homology
Function and homology information


alcohol dehydrogenase (NADP+) / alcohol dehydrogenase (NADP+) activity
Similarity search - Function
NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ADENOSINE MONOPHOSPHATE / BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / PHOSPHATE ION / Aldehyde reductase 2
Similarity search - Component
Biological speciesSporidiobolus salmonicolor (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsKamitori, S. / Kita, K.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: X-ray Structures of NADPH-dependent Carbonyl Reductase from Sporobolomyces salmonicolor Provide Insights into Stereoselective Reductions of Carbonyl Compounds
Authors: Kamitori, S. / Iguchi, A. / Ohtaki, A. / Yamada, M. / Kita, K.
History
DepositionNov 19, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Aldehyde reductase II
B: Aldehyde reductase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,25611
Polymers74,4502
Non-polymers1,8069
Water13,205733
1
A: Aldehyde reductase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1586
Polymers37,2251
Non-polymers9335
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aldehyde reductase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0995
Polymers37,2251
Non-polymers8734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.000, 83.391, 148.324
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Aldehyde reductase II / Aldose reductase / ARII


Mass: 37225.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sporidiobolus salmonicolor (yeast) / Plasmid: pUCAR2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q9UUN9, alcohol dehydrogenase (NADP+)

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Non-polymers , 6 types, 742 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-NMN / BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / NICOTINAMIDE MONONUCLEOTIDE / Nicotinamide mononucleotide


Mass: 335.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H16N2O8P
#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 733 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 32% (w/v) polyethylene glycol 2000 MME, 100mM ammonium sulfate and 200mM sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-6A11
SYNCHROTRONPhoton Factory AR-NW12A20.9789
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDOct 21, 2003
ADSC QUANTUM 42CCD
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97891
ReflectionResolution: 1.6→74.16 Å / Num. all: 84533 / Num. obs: 84533 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.4 Å2
Reflection shellResolution: 1.6→1.7 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→74.16 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2192638.41 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.239 8508 10.1 %RANDOM
Rwork0.217 ---
all0.22 84533 --
obs0.217 84533 93.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.7925 Å2 / ksol: 0.343688 e/Å3
Displacement parametersBiso mean: 18.2 Å2
Baniso -1Baniso -2Baniso -3
1-4.04 Å20 Å20 Å2
2---1.1 Å20 Å2
3----2.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.6→74.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5251 0 110 733 6094
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.111.5
X-RAY DIFFRACTIONc_mcangle_it1.682
X-RAY DIFFRACTIONc_scbond_it1.82
X-RAY DIFFRACTIONc_scangle_it2.562.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.264 1516 10.1 %
Rwork0.232 13427 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
X-RAY DIFFRACTION4NADPH.PARAMNADPH.TOP

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