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- PDB-6t27: Structure of Human Aldose Reductase Mutant L301A with a Citrate M... -

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Basic information

Entry
Database: PDB / ID: 6t27
TitleStructure of Human Aldose Reductase Mutant L301A with a Citrate Molecule Bound in the Anion Binding Pocket
ComponentsAldo-keto reductase family 1 member B1
KeywordsOXIDOREDUCTASE / L301A Mutant / Citrate Complex
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
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: 1.11 Å
AuthorsHubert, L.-S. / Ley, M. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: Structure of Human Aldose Reductase Mutant L301A with a Citrate Molecule Bound in the Anion Binding Pocket
Authors: Hubert, L.-S. / Ley, M. / Heine, A. / Klebe, G.
History
DepositionOct 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2020Provider: 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)36,9844
Polymers35,8561
Non-polymers1,1283
Water7,800433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-2 kcal/mol
Surface area12840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.266, 66.625, 49.345
Angle α, β, γ (deg.)90.000, 92.072, 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: 35856.262 Da / Num. of mol.: 1 / Mutation: L301A
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-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 433 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.15 Å3/Da / Density % sol: 42.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 50 mM Di-Ammoniumhydrogen citrate pH 5: 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, 20% (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 PILATUS3 6M / Detector: PIXEL / Date: Aug 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.11→47.24 Å / Num. obs: 111606 / % possible obs: 92.3 % / Redundancy: 3.9 % / Biso Wilson estimate: 7.57 Å2 / CC1/2: 0.998 / Rsym value: 0.045 / Net I/σ(I): 17.76
Reflection shellResolution: 1.11→1.18 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 6.79 / Num. unique obs: 17437 / CC1/2: 0.972 / Rsym value: 0.162 / % possible all: 89.3

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Processing

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

4prr


Resolution: 1.11→47.24 Å / SU ML: 0.059 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 8.8265
RfactorNum. reflection% reflection
Rfree0.1213 5579 5 %
Rwork0.1037 --
obs0.1045 111601 92.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 11.11 Å2
Refinement stepCycle: LAST / Resolution: 1.11→47.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2473 0 74 433 2980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00622885
X-RAY DIFFRACTIONf_angle_d1.00443981
X-RAY DIFFRACTIONf_chiral_restr0.2411438
X-RAY DIFFRACTIONf_plane_restr0.0081543
X-RAY DIFFRACTIONf_dihedral_angle_d19.2861096
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.11-1.120.13311710.10793264X-RAY DIFFRACTION84.21
1.12-1.130.12021810.09933446X-RAY DIFFRACTION91.29
1.13-1.150.13481820.09463452X-RAY DIFFRACTION90.15
1.15-1.160.1091810.09393440X-RAY DIFFRACTION91.07
1.16-1.180.11311820.09563461X-RAY DIFFRACTION89.8
1.18-1.190.13651700.09693230X-RAY DIFFRACTION85.6
1.19-1.210.12071870.08813555X-RAY DIFFRACTION92.26
1.21-1.230.09361830.08433478X-RAY DIFFRACTION91.92
1.23-1.250.11511860.0873532X-RAY DIFFRACTION92.63
1.25-1.270.11571860.09033535X-RAY DIFFRACTION91.79
1.27-1.290.11411850.08743510X-RAY DIFFRACTION92.56
1.29-1.310.10651890.09013580X-RAY DIFFRACTION92.83
1.31-1.340.11981840.09093499X-RAY DIFFRACTION91.8
1.34-1.370.12581790.09423401X-RAY DIFFRACTION89.23
1.37-1.40.11991820.08763455X-RAY DIFFRACTION90.61
1.4-1.430.10531890.08593603X-RAY DIFFRACTION94.07
1.43-1.460.11121900.08193596X-RAY DIFFRACTION94.32
1.46-1.50.10151890.0823600X-RAY DIFFRACTION93.81
1.5-1.550.11191900.08173617X-RAY DIFFRACTION94.28
1.55-1.60.09841890.0813579X-RAY DIFFRACTION93.99
1.6-1.660.11171880.08483581X-RAY DIFFRACTION93.45
1.66-1.720.10571770.08953366X-RAY DIFFRACTION88.13
1.72-1.80.10791930.09323667X-RAY DIFFRACTION95.78
1.8-1.90.11531940.09933679X-RAY DIFFRACTION95.32
1.9-2.010.12441920.10293647X-RAY DIFFRACTION95.76
2.01-2.170.12691920.10323655X-RAY DIFFRACTION94.89
2.17-2.390.11761840.10853488X-RAY DIFFRACTION90.82
2.39-2.730.13881930.11893662X-RAY DIFFRACTION95.3
2.73-3.440.14571980.1283759X-RAY DIFFRACTION97.13
3.44-47.240.12581930.13143685X-RAY DIFFRACTION93.47

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