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- PDB-6ky6: Crystal structure of a thermostable aldo-keto reductase Tm1743 in... -

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Basic information

Entry
Database: PDB / ID: 6ky6
TitleCrystal structure of a thermostable aldo-keto reductase Tm1743 in complexs with inhibitor epalrestat in space group P3221cc
Components2,5-diketo-D-gluconic acid reductase
KeywordsOXIDOREDUCTASE / Aldo-ketone reductase / Tolrestat / Epalrestat / Competitive inhibitor
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
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
Chem-EPR / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Oxidoreductase, aldo/keto reductase family
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsZhang, C.Y. / Min, Z.Z. / Liu, X.M. / Wang, C. / Tang, W.R.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570738 China
National Natural Science Foundation of China31870740 China
National Natural Science Foundation of China31400630 China
CitationJournal: Febs Lett. / Year: 2020
Title: Tolrestat acts atypically as a competitive inhibitor of the thermostable aldo-keto reductase Tm1743 from Thermotoga maritima.
Authors: Zhang, C. / Min, Z. / Liu, X. / Wang, C. / Wang, Z. / Shen, J. / Tang, W. / Zhang, X. / Liu, D. / Xu, X.
History
DepositionSep 16, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 13, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Nov 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: 2,5-diketo-D-gluconic acid reductase
B: 2,5-diketo-D-gluconic acid reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,10911
Polymers62,8062
Non-polymers2,3039
Water5,495305
1
A: 2,5-diketo-D-gluconic acid reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5375
Polymers31,4031
Non-polymers1,1344
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-12 kcal/mol
Surface area12560 Å2
MethodPISA
2
B: 2,5-diketo-D-gluconic acid reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5726
Polymers31,4031
Non-polymers1,1695
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-11 kcal/mol
Surface area12490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.128, 84.128, 185.765
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein 2,5-diketo-D-gluconic acid reductase / Oxidoreductase / aldo/keto reductase family


Mass: 31402.947 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_1743, Tmari_1751 / Plasmid: pET-28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9X265
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EPR / {5-[(2E)-2-methyl-3-phenylprop-2-en-1-ylidene]-4-oxo-2-thioxo-1,3-thiazolidin-3-yl}acetic acid / Epalrestat / Epalrestat


Mass: 319.399 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H13NO3S2 / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.01 Å3/Da / Density % sol: 59.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 100000, 0.1 M sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. obs: 47061 / % possible obs: 100 % / Redundancy: 10.4 % / Rpim(I) all: 0.058 / Rrim(I) all: 0.186 / Χ2: 1.509 / Net I/σ(I): 26.63
Reflection shellResolution: 2.07→2.11 Å / Mean I/σ(I) obs: 5.423 / Num. unique obs: 226 / Rpim(I) all: 0.303 / Rrim(I) all: 0.977 / Χ2: 0.732 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DAN

5dan


Resolution: 2.07→47.23 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.713 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.201 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2561 2364 5 %RANDOM
Rwork0.2173 ---
obs0.2193 44894 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.07 Å2 / Biso mean: 27.423 Å2 / Biso min: 10.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20.27 Å20 Å2
2--0.54 Å2-0 Å2
3----1.75 Å2
Refinement stepCycle: final / Resolution: 2.07→47.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4412 0 125 305 4842
Biso mean--44.84 39.33 -
Num. residues----548
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0154635
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174229
X-RAY DIFFRACTIONr_angle_refined_deg1.461.7826282
X-RAY DIFFRACTIONr_angle_other_deg0.4491.7139934
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.885550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.88816.753154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.72815692
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6341538
X-RAY DIFFRACTIONr_chiral_restr0.0620.2598
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215097
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02805
LS refinement shellResolution: 2.07→2.124 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 150 -
Rwork0.269 3290 -
all-3440 -
obs--99.48 %

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