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- PDB-4ga8: Human AKR1B10 mutant V301L complexed with NADP+ and sorbinil -

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Basic information

Entry
Database: PDB / ID: 4ga8
TitleHuman AKR1B10 mutant V301L complexed with NADP+ and sorbinil
ComponentsAldo-keto reductase family 1 member B10
KeywordsOXIDOREDUCTASE / tim barrel / aldo-keto reductase
Function / homology
Function and homology information


indanol dehydrogenase activity / alcohol dehydrogenase (NADP+) activity / farnesol catabolic process / geranylgeranyl reductase activity / cellular detoxification of aldehyde / NADP-retinol dehydrogenase / : / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / all-trans-retinol dehydrogenase (NADP+) activity ...indanol dehydrogenase activity / alcohol dehydrogenase (NADP+) activity / farnesol catabolic process / geranylgeranyl reductase activity / cellular detoxification of aldehyde / NADP-retinol dehydrogenase / : / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / all-trans-retinol dehydrogenase (NADP+) activity / daunorubicin metabolic process / doxorubicin metabolic process / retinal dehydrogenase (NAD+) activity / aldose reductase (NADPH) activity / retinoid metabolic process / Retinoid metabolism and transport / lysosome / mitochondrion / extracellular region / cytosol
Similarity search - Function
Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / 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 putative active site signature. / Aldo/keto reductase family signature 1. / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / SORBINIL / Aldo-keto reductase family 1 member B10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.942 Å
AuthorsCousido-Siah, A. / Ruiz Figueras, F.X. / Mitschler, A. / Podjarny, A.
History
DepositionJul 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldo-keto reductase family 1 member B10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0653
Polymers36,0861
Non-polymers9802
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.300, 89.300, 78.155
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Aldo-keto reductase family 1 member B10 / ARL-1 / Aldose reductase-like / Aldose reductase-related protein / ARP / hARP / Small intestine ...ARL-1 / Aldose reductase-like / Aldose reductase-related protein / ARP / hARP / Small intestine reductase / SI reductase


Mass: 36085.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1B10, AKR1B11 / Plasmid: pET30-Xa/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O60218, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-SBI / SORBINIL


Mass: 236.199 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H9FN2O3 / Comment: inhibitor*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 50.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 30% PEG 6000, 100 mM SODIUM CACODYLATE, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Dec 16, 2009 / Details: OSMIC MIRRORS
RadiationMonochromator: DOUBLE MIRRORS MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.942→50 Å / Num. all: 26194 / Num. obs: 26168 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 26.596 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Χ2: 0.975 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.942-2.025.40.4625970.821199.9
2.02-2.15.50.35526051.0431100
2.1-2.25.80.24825970.9041100
2.2-2.316.10.21726111.081100
2.31-2.466.50.1625910.9511100
2.46-2.656.80.13426320.8881100
2.65-2.917.10.10526220.9561100
2.91-3.337.40.07626200.9531100
3.33-4.27.60.05826210.9651100
4.2-507.80.03926721.136199.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
AMoREphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZUA

1zua


Resolution: 1.942→24.481 Å / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.8602 / SU ML: 0.22 / Cross valid method: R-free / σ(F): 1.34 / Phase error: 21.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1329 5.08 %5 % random
Rwork0.1509 ---
obs0.1538 26139 99.82 %-
all-26186 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.56 Å2 / Biso mean: 25.9935 Å2 / Biso min: 8.87 Å2
Refinement stepCycle: LAST / Resolution: 1.942→24.481 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2546 0 65 336 2947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072871
X-RAY DIFFRACTIONf_angle_d1.2763929
X-RAY DIFFRACTIONf_chiral_restr0.079420
X-RAY DIFFRACTIONf_plane_restr0.006507
X-RAY DIFFRACTIONf_dihedral_angle_d12.9321094
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.942-2.01970.26281300.20232724285499
2.0197-2.11160.28841510.177327412892100
2.1116-2.22280.23181510.170227422893100
2.2228-2.3620.22821370.16827522889100
2.362-2.54420.21221460.165927642910100
2.5442-2.79990.20341540.170327582912100
2.7999-3.20430.22931500.161127602910100
3.2043-4.03410.20711520.134127552907100
4.0341-24.48330.16031580.123628142972100

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