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- PDB-6t5g: Structure of Human Aldose Reductase Mutant L300A with a Citrate M... -

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Basic information

Entry
Database: PDB / ID: 6t5g
TitleStructure of Human Aldose Reductase Mutant L300A with a Citrate Molecule Bound in the Anion Binding Pocket
ComponentsAldo-keto reductase family 1 member B1
KeywordsOXIDOREDUCTASE / L300A 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: 1.28 Å
AuthorsHubert, L.-S. / Ley, M. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: Structure of Human Aldose Reductase Mutant L300A with a Citrate Molecule Bound in the Anion Binding Pocket
Authors: Hubert, L.-S. / Ley, M. / Heine, A. / Klebe, G.
History
DepositionOct 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 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
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-3 kcal/mol
Surface area12500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.685, 46.717, 48.507
Angle α, β, γ (deg.)93.012, 116.859, 102.606
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,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: L300A
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.: 301 / 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: 2.14 Å3/Da / Density % sol: 42.48 %
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 6006

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979003 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979003 Å / Relative weight: 1
ReflectionResolution: 1.277→44.9 Å / Num. obs: 69706 / % possible obs: 89.6 % / Redundancy: 2 % / Biso Wilson estimate: 10.5 Å2 / CC1/2: 0.986 / Rsym value: 0.082 / Net I/σ(I): 6.11
Reflection shellResolution: 1.28→1.35 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.42 / Num. unique obs: 10022 / CC1/2: 0.793 / Rsym value: 0.288 / % possible all: 79.9

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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: 1.28→44.9 Å / SU ML: 0.1197 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 16.1877
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1595 3486 5 %
Rwork0.1296 66212 -
obs0.1311 69698 89.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.53 Å2
Refinement stepCycle: LAST / Resolution: 1.28→44.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2454 0 74 301 2829
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01172694
X-RAY DIFFRACTIONf_angle_d1.23763700
X-RAY DIFFRACTIONf_chiral_restr0.0874417
X-RAY DIFFRACTIONf_plane_restr0.0094469
X-RAY DIFFRACTIONf_dihedral_angle_d18.7105989
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.28-1.290.2783930.22291755X-RAY DIFFRACTION59.54
1.29-1.310.23941330.21072525X-RAY DIFFRACTION85.69
1.31-1.330.24021360.18662596X-RAY DIFFRACTION87.68
1.33-1.350.23431340.1762533X-RAY DIFFRACTION86.9
1.35-1.380.23791370.17072601X-RAY DIFFRACTION86.84
1.38-1.40.22691330.16472538X-RAY DIFFRACTION87.55
1.4-1.420.19661380.16252611X-RAY DIFFRACTION86.97
1.42-1.450.19911350.14942572X-RAY DIFFRACTION88.84
1.45-1.480.19161390.13492648X-RAY DIFFRACTION89.79
1.48-1.510.15571440.12082726X-RAY DIFFRACTION91.46
1.51-1.550.16051410.11512684X-RAY DIFFRACTION91.96
1.55-1.590.16011420.10692702X-RAY DIFFRACTION91.74
1.59-1.630.14911470.10352780X-RAY DIFFRACTION93.72
1.63-1.680.14511430.10372721X-RAY DIFFRACTION92.27
1.68-1.730.16571450.10312752X-RAY DIFFRACTION92.09
1.73-1.790.14011440.10592740X-RAY DIFFRACTION92.67
1.79-1.870.1531430.10652722X-RAY DIFFRACTION92.84
1.87-1.950.13721440.11042739X-RAY DIFFRACTION93.15
1.95-2.050.13961440.11152730X-RAY DIFFRACTION93.22
2.05-2.180.13471460.11072762X-RAY DIFFRACTION93.26
2.18-2.350.13721440.122751X-RAY DIFFRACTION93.21
2.35-2.590.1541460.12792770X-RAY DIFFRACTION93.91
2.59-2.960.1531440.13552740X-RAY DIFFRACTION93.27
2.96-3.730.15111450.13672749X-RAY DIFFRACTION93.51
3.73-44.90.15891460.14342765X-RAY DIFFRACTION93.33

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