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- PDB-5zcm: Crystal structure of Xylose reductase from Debaryomyces nepalensi... -

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Basic information

Entry
Database: PDB / ID: 5zcm
TitleCrystal structure of Xylose reductase from Debaryomyces nepalensis in complex with NADP-DTT adduct
ComponentsAldose reductase
KeywordsOXIDOREDUCTASE / Carbohydrate metabolism / aldo-keto reductase / TIM barrel
Function / homology
Function and homology information


D-xylose reductase [NAD(P)H] / D-xylose reductase (NADPH) activity / D-xylose catabolic process / nucleotide binding
Similarity search - Function
Aldo-keto reductase family 2B / Aldo/keto reductase family putative active site signature. / 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 ...Aldo-keto reductase family 2B / Aldo/keto reductase family putative active site signature. / 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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Chem-NDP / D-xylose reductase [NAD(P)H]
Similarity search - Component
Biological speciesDebaryomyces nepalensis (yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsManoj, N.
Citation
Journal: FEBS J. / Year: 2018
Title: Crystal structure of yeast xylose reductase in complex with a novel NADP-DTT adduct provides insights into substrate recognition and catalysis.
Authors: Paidimuddala, B. / Mohapatra, S.B. / Gummadi, S.N. / Manoj, N.
#1: Journal: RSC Adv. / Year: 2017
Title: A halotolerant aldose reductase fromDebaryomyces nepalensis: gene isolation,overexpression and biochemical characterization
Authors: Paidimuddala, B. / Aradhyam, G.K. / Gummadi, S.N.
History
DepositionFeb 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aldose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8203
Polymers38,9201
Non-polymers9002
Water5,549308
1
A: Aldose reductase
hetero molecules

A: Aldose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6406
Polymers77,8412
Non-polymers1,7994
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area5930 Å2
ΔGint-28 kcal/mol
Surface area25960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.590, 108.220, 71.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-587-

HOH

21A-620-

HOH

31A-790-

HOH

41A-797-

HOH

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Components

#1: Protein Aldose reductase


Mass: 38920.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Debaryomyces nepalensis (yeast) / Gene: AR / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: A0A0M4HL56, aldose reductase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.49 Å3/Da / Density % sol: 50.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 35% PEG 3000, 1 M HEPES (pH 7.5), 1.5 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 18, 2017
RadiationMonochromator: Double mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→36.641 Å / Num. obs: 42718 / % possible obs: 99.4 % / Redundancy: 13.3 % / Biso Wilson estimate: 13.54 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.043 / Rrim(I) all: 0.158 / Net I/σ(I): 13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.7-1.7313.10.80221920.7060.2260.83498.3
9-36.6412.20.0583360.9980.0170.06198.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.4data scaling
PHASERphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZCI

5zci


Resolution: 1.7→36.641 Å / SU ML: 0.18 / SU R Cruickshank DPI: 0.1143 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 16.59
RfactorNum. reflection% reflectionSelection details
Rfree0.1851 2106 4.93 %Random selection
Rwork0.1624 ---
obs0.1636 42699 99.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 49.86 Å2 / Biso mean: 16.92 Å2 / Biso min: 6.01 Å2
Refine analyzeLuzzati coordinate error obs: 0.1646 Å
Refinement stepCycle: final / Resolution: 1.7→36.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2627 0 81 308 3016
Biso mean--16.98 20.96 -
Num. residues----329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012780
X-RAY DIFFRACTIONf_angle_d1.1123787
X-RAY DIFFRACTIONf_chiral_restr0.058410
X-RAY DIFFRACTIONf_plane_restr0.008485
X-RAY DIFFRACTIONf_dihedral_angle_d12.5511647
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.73960.29021490.25092639278898
1.7396-1.78310.2481410.21922626276798
1.7831-1.83130.24021200.20262672279298
1.8313-1.88520.23951370.18962673281098
1.8852-1.9460.2051150.19142687280299
1.946-2.01550.19151190.16332698281799
2.0155-2.09620.19461530.16182687284099
2.0962-2.19160.18991530.15972642279599
2.1916-2.30720.18181590.162227092868100
2.3072-2.45170.18231600.150626952855100
2.4517-2.64090.17171110.144527492860100
2.6409-2.90660.17391340.149927272861100
2.9066-3.32690.17791510.160427432894100
3.3269-4.19060.16791260.143327922918100
4.1906-36.64950.15091780.152428543032100

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