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- PDB-4ijc: Crystal structure of arabinose dehydrogenase Ara1 from Saccharomy... -

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Basic information

Entry
Database: PDB / ID: 4ijc
TitleCrystal structure of arabinose dehydrogenase Ara1 from Saccharomyces cerevisiae
ComponentsD-arabinose dehydrogenase [NAD(P)+] heavy chain
KeywordsOXIDOREDUCTASE / BETA BARREL / TIM barrel
Function / homology
Function and homology information


D-arabinose 1-dehydrogenase [NAD(P)+] / D-arabinose 1-dehydrogenase (NAD+) activity / Estrogen biosynthesis / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Pregnenolone biosynthesis / Fructose biosynthesis / Formation of xylulose-5-phosphate / Prednisone ADME / D-arabinose 1-dehydrogenase [NAD(P)+] activity ...D-arabinose 1-dehydrogenase [NAD(P)+] / D-arabinose 1-dehydrogenase (NAD+) activity / Estrogen biosynthesis / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Pregnenolone biosynthesis / Fructose biosynthesis / Formation of xylulose-5-phosphate / Prednisone ADME / D-arabinose 1-dehydrogenase [NAD(P)+] activity / D-arabinose 1-dehydrogenase (NADP+) activity / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / Glycogen breakdown (glycogenolysis) / RA biosynthesis pathway / acetoin metabolic process / Glutathione conjugation / diacetyl reductase ((S)-acetoin forming) (NAD+) activity / aldose reductase (NADPH) activity / carbohydrate metabolic process / cytosol
Similarity search - Function
Aldo-keto reductase family 3C1 / 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 3C1 / 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
D-arabinose dehydrogenase [NAD(P)+] heavy chain
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHu, X.Q. / Guo, P.C. / Li, W.F. / Zhou, C.Z.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Structures of Saccharomyces cerevisiaeD-arabinose dehydrogenase Ara1 and its complex with NADPH: implications for cofactor-assisted substrate recognition
Authors: Hu, X.Q. / Guo, P.C. / Ma, J.D. / Li, W.F.
History
DepositionDec 21, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: D-arabinose dehydrogenase [NAD(P)+] heavy chain
B: D-arabinose dehydrogenase [NAD(P)+] heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3417
Polymers77,8652
Non-polymers4765
Water6,089338
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.898, 91.568, 107.643
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 D-arabinose dehydrogenase [NAD(P)+] heavy chain / AKR3C / NADP+ dependent arabinose dehydrogenase


Mass: 38932.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: s288c / Gene: ARA1, YBR1127, YBR149W / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P38115, D-arabinose 1-dehydrogenase [NAD(P)+]
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.24 Å3/Da / Density % sol: 45.18 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% polyethylene glycol 3350, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.919 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 41412 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 19.557
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 10 / Rsym value: 0.257 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZUA

1zua


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.919 / SU B: 11.81 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26394 2084 5 %RANDOM
Rwork0.22322 ---
obs0.22527 39323 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.911 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å20 Å2
2---2.44 Å20 Å2
3---1.93 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5288 0 26 338 5652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225437
X-RAY DIFFRACTIONr_angle_refined_deg0.9851.9857383
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.995658
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.49124.545242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.39615958
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4231526
X-RAY DIFFRACTIONr_chiral_restr0.0660.2822
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214074
X-RAY DIFFRACTIONr_mcbond_it0.2841.53304
X-RAY DIFFRACTIONr_mcangle_it0.55125370
X-RAY DIFFRACTIONr_scbond_it0.89832133
X-RAY DIFFRACTIONr_scangle_it1.5184.52013
LS refinement shellResolution: 2.102→2.157 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 140 -
Rwork0.222 2777 -
obs--96.72 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.72860.4029-0.17672.0471-0.41340.74730.1537-0.08150.07540.2099-0.1208-0.0751-0.09540.0303-0.03290.0988-0.05080.01240.1371-0.02010.019424.96617.89215.015
20.76260.3080.17141.47820.22710.98680.148-0.0955-0.12330.068-0.07920.0530.0924-0.0669-0.06880.08-0.0514-0.03610.12260.04050.045911.23-18.11114.397
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 344
2X-RAY DIFFRACTION2B15 - 344

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