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- PDB-1hqt: THE CRYSTAL STRUCTURE OF AN ALDEHYDE REDUCTASE Y50F MUTANT-NADP C... -

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Basic information

Entry
Database: PDB / ID: 1hqt
TitleTHE CRYSTAL STRUCTURE OF AN ALDEHYDE REDUCTASE Y50F MUTANT-NADP COMPLEX AND ITS IMPLICATIONS FOR SUBSTRATE BINDING
ComponentsALDEHYDE REDUCTASE
KeywordsOXIDOREDUCTASE / alpha/beta barrel TIM barrel holo enzyme
Function / homology
Function and homology information


glucuronate reductase / glucuronolactone reductase / glucuronolactone reductase activity / Oxidoreductases; Acting on NADH or NADPH / S-nitrosoglutathione reductase (NADPH) activity / alcohol dehydrogenase (NADP+) / D-glucuronate catabolic process / L-ascorbic acid biosynthetic process / aldehyde catabolic process / methylglyoxal reductase (NADPH) (acetol producing) activity ...glucuronate reductase / glucuronolactone reductase / glucuronolactone reductase activity / Oxidoreductases; Acting on NADH or NADPH / S-nitrosoglutathione reductase (NADPH) activity / alcohol dehydrogenase (NADP+) / D-glucuronate catabolic process / L-ascorbic acid biosynthetic process / aldehyde catabolic process / methylglyoxal reductase (NADPH) (acetol producing) activity / cellular detoxification of aldehyde / L-glucuronate reductase activity / D/L-glyceraldehyde reductase / glycerol dehydrogenase (NADP+) activity / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / aldose reductase (NADPH) activity / lipid metabolic process / apical plasma membrane / cytosol
Similarity search - Function
Aldo-keto reductase family 1 member A1 / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily ...Aldo-keto reductase family 1 member A1 / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldo-keto reductase family 1 member A1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsYe, Q. / Hyndman, D. / Green, N.C. / Li, L. / Korithoski, B. / Jia, Z. / Flynn, T.G.
CitationJournal: Chem.Biol.Interact. / Year: 2001
Title: The Crystal Structure of an Aldehyde Reductase Y50F Mutant-NADP Complex and its Implications for Substrate Binding
Authors: Ye, Q. / Hyndman, D. / Green, N.C. / Li, L. / Jia, Z. / Flynn, T.G.
History
DepositionDec 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALDEHYDE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4762
Polymers36,7331
Non-polymers7431
Water4,810267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.29, 70.12, 92.72
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ALDEHYDE REDUCTASE / ALCOHOL DEHYDROGENASE [NADP+]


Mass: 36733.059 Da / Num. of mol.: 1 / Mutation: Y50F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Plasmid: PET16B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P50578, alcohol dehydrogenase (NADP+)
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.36 Å3/Da / Density % sol: 47.8 %
Crystal growTemperature: 277 K / Method: evaporation
Details: PEG 6000, NaCl, MES, EVAPORATION, temperature 277.0K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / PH range low: 7.5 / PH range high: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-8 %PEG60001drop
225 mMMES1drop
31-1.5 M1reservoirNaCl
4100 mMMES1reservoir
510 mg/mlprotein1drop
649 mMNADPH1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1998
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→6 Å / Num. all: 42437 / Num. obs: 17569 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rsym value: 0.072 / Net I/σ(I): 11.04
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 3.43 / Num. unique all: 17569 / Rsym value: 0.266 / % possible all: 92.6
Reflection
*PLUS
Num. measured all: 42437

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Processing

Software
NameClassification
EPMRphasing
CNSrefinement
MAR345data collection
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ossama EI-Kabbani, personal communication.

Resolution: 2.2→6 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.296 1492 -random
Rwork0.212 ---
all0.213 14901 --
obs0.213 17254 86.4 %-
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2571 0 48 267 2886
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.28
LS refinement shellResolution: 2.2→6 Å
RfactorNum. reflection% reflection
Rfree0.296 1492 -
Rwork0.212 --
obs-14901 86.4 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 6 Å / σ(F): 0 / Rfactor obs: 0.212
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 6 Å / Rfactor Rfree: 0.296 / Rfactor Rwork: 0.212

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