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- PDB-6xum: Human Aldose Reductase Mutant L300/301A in Complex with a Ligand ... -

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Entry
Database: PDB / ID: 6xum
TitleHuman Aldose Reductase Mutant L300/301A in Complex with a Ligand with an IDD Structure ({5-fluoro-2-[(3-nitrobenzyl)carbamoyl]phenoxy}acetic acid)
ComponentsAldo-keto reductase family 1 member B1
KeywordsOXIDOREDUCTASE / L300/301A Mutant / IDD_06 / Opened Transient Pocket / hAR
Function / homology
Function and homology information


glyceraldehyde oxidoreductase activity / Fructose biosynthesis / fructose biosynthetic process / L-glucuronate reductase activity / glycerol dehydrogenase [NADP+] activity / D/L-glyceraldehyde reductase / aldose reductase / C21-steroid hormone biosynthetic process / Pregnenolone biosynthesis / NADP-retinol dehydrogenase ...glyceraldehyde oxidoreductase activity / Fructose biosynthesis / fructose biosynthetic process / L-glucuronate reductase activity / glycerol dehydrogenase [NADP+] activity / D/L-glyceraldehyde reductase / aldose reductase / C21-steroid hormone biosynthetic process / Pregnenolone biosynthesis / NADP-retinol dehydrogenase / L-ascorbic acid biosynthetic process / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / metanephric collecting duct development / prostaglandin H2 endoperoxidase reductase activity / regulation of urine volume / all-trans-retinol dehydrogenase (NADP+) activity / renal water homeostasis / epithelial cell maturation / daunorubicin metabolic process / doxorubicin metabolic process / retinal dehydrogenase activity / aldose reductase (NADPH) activity / retinoid metabolic process / cellular hyperosmotic salinity response / electron transfer activity / carbohydrate metabolic process / negative regulation of apoptotic process / extracellular space / extracellular exosome / nucleoplasm / cytosol
Similarity search - Function
Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / 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
Similarity search - Domain/homology
Chem-30L / CITRIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldo-keto reductase family 1 member B1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.97 Å
AuthorsHubert, L.-S. / Ley, M. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: Human Aldose Reductase Mutant L300/301A in Complex with a Ligand with an IDD Structure ({5-fluoro-2-[(3-nitrobenzyl)carbamoyl]phenoxy}acetic acid)
Authors: Hubert, L.-S. / Ley, M. / Scheer, F. / Diederich, W. / Heine, A. / Klebe, G.
History
DepositionJan 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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: Aldo-keto reductase family 1 member B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0984
Polymers35,8141
Non-polymers1,2843
Water6,666370
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-5 kcal/mol
Surface area12730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.288, 66.739, 49.378
Angle α, β, γ (deg.)90.000, 92.220, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Aldo-keto reductase family 1 member B1 / Aldehyde reductase / Aldose reductase / AR


Mass: 35814.184 Da / Num. of mol.: 1 / Mutation: L300/301A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1B1, ALDR1, ALR2 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold
References: UniProt: P15121, NADP-retinol dehydrogenase, D/L-glyceraldehyde reductase, allyl-alcohol dehydrogenase, aldose reductase
#2: Chemical ChemComp-30L / {5-fluoro-2-[(3-nitrobenzyl)carbamoyl]phenoxy}acetic acid


Mass: 348.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H13FN2O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


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


Mass: 18.015 Da / Num. of mol.: 370 / 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: 2.16 Å3/Da / Density % sol: 43.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 50 mM Di-Ammoniumhydrogen citrate pH 5.0: 15 mg/mL hAR, 5.2 mg/mL DTT, 0.7 mg/mL NADP+, 5% (w/v) PEG 6000 Reservoir: 120 mM Di-Ammoniumhydrogen citrate pH 5.0, 20% (w/v) PEG 6000 Soaking- ...Details: 50 mM Di-Ammoniumhydrogen citrate pH 5.0: 15 mg/mL hAR, 5.2 mg/mL DTT, 0.7 mg/mL NADP+, 5% (w/v) PEG 6000 Reservoir: 120 mM Di-Ammoniumhydrogen citrate pH 5.0, 20% (w/v) PEG 6000 Soaking-buffer: 120 mM Di-Ammoniumhydrogen citrate pH 5.0, 25% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 0.969→38.565 Å / Num. obs: 175185 / % possible obs: 96.8 % / Redundancy: 3.67 % / Biso Wilson estimate: 7.91 Å2 / CC1/2: 0.999 / Rsym value: 0.036 / Net I/σ(I): 17.81
Reflection shellResolution: 0.97→1.03 Å / Redundancy: 3.45 % / Mean I/σ(I) obs: 2.39 / Num. unique obs: 27480 / CC1/2: 0.795 / Rsym value: 0.471 / % possible all: 93.9

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Cootmodel building
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PRR

4prr


Resolution: 0.97→38.56 Å / SU ML: 0.0693 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 10.686
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1279 8759 5 %
Rwork0.1188 166413 -
obs0.1192 175172 96.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.6 Å2
Refinement stepCycle: LAST / Resolution: 0.97→38.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2460 0 86 370 2916
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00622923
X-RAY DIFFRACTIONf_angle_d0.9924031
X-RAY DIFFRACTIONf_chiral_restr0.0804441
X-RAY DIFFRACTIONf_plane_restr0.0079565
X-RAY DIFFRACTIONf_dihedral_angle_d15.81041118
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.97-0.980.24772730.23265168X-RAY DIFFRACTION91.14
0.98-0.990.22962840.22065395X-RAY DIFFRACTION94.27
0.99-10.212870.20295464X-RAY DIFFRACTION95.03
1-1.020.19822840.18125392X-RAY DIFFRACTION94.85
1.02-1.030.18872860.16925430X-RAY DIFFRACTION94.35
1.03-1.040.16292800.16075322X-RAY DIFFRACTION94.02
1.04-1.060.15682890.14065489X-RAY DIFFRACTION95.68
1.06-1.070.13732910.12365539X-RAY DIFFRACTION95.98
1.07-1.090.11312880.11275471X-RAY DIFFRACTION96.27
1.09-1.110.11282890.10685488X-RAY DIFFRACTION96.61
1.11-1.130.11532910.10385536X-RAY DIFFRACTION96.44
1.13-1.150.12912910.10055515X-RAY DIFFRACTION96.45
1.15-1.170.12082870.09685467X-RAY DIFFRACTION95.25
1.17-1.20.10422910.09395529X-RAY DIFFRACTION97.16
1.2-1.220.10322950.09235600X-RAY DIFFRACTION97.12
1.22-1.250.11632920.09375534X-RAY DIFFRACTION97.28
1.25-1.280.10272950.09325608X-RAY DIFFRACTION97.36
1.28-1.320.11332950.09285612X-RAY DIFFRACTION97.96
1.32-1.350.11352950.09155594X-RAY DIFFRACTION98.04
1.35-1.40.11692930.09565569X-RAY DIFFRACTION97.29
1.4-1.450.10812940.09265596X-RAY DIFFRACTION97.69
1.45-1.510.11562980.09495662X-RAY DIFFRACTION98.54
1.51-1.570.11722970.09345645X-RAY DIFFRACTION98.48
1.57-1.660.10983000.09745694X-RAY DIFFRACTION99.07
1.66-1.760.12092990.10685686X-RAY DIFFRACTION98.96
1.76-1.90.12342980.11075653X-RAY DIFFRACTION97.99
1.9-2.090.1382930.11775578X-RAY DIFFRACTION97.28
2.09-2.390.12213000.12165689X-RAY DIFFRACTION98.68
2.39-3.010.12733010.13485723X-RAY DIFFRACTION98.84
3.01-38.560.13663030.13985765X-RAY DIFFRACTION98.33

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