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- PDB-3qkz: Crystal structure of mutant His269Arg AKR1B14 -

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Basic information

Entry
Database: PDB / ID: 3qkz
TitleCrystal structure of mutant His269Arg AKR1B14
ComponentsAldo-keto reductase family 1, member B7
KeywordsOXIDOREDUCTASE / Aldose reductase-like proteins / AKR1B14
Function / homology
Function and homology information


Estrogen biosynthesis / aldo-keto reductase (NADPH) activity / aldose reductase / prostaglandin H2 endoperoxidase reductase activity / aldose reductase (NADPH) activity / mitochondrion / cytosol
Similarity search - Function
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 / Aldo-keto reductase family 1 member B7
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsSundaram, K. / El-Kabbani, O.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Structure of the His269Arg mutant of the rat aldose reductase-like protein AKR1B14 complexed with NADPH.
Authors: Sundaram, K. / Endo, S. / Matsunaga, T. / Tanaka, N. / Hara, A. / El-Kabbani, O.
History
DepositionFeb 2, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1May 2, 2012Group: Database references
Revision 1.2Nov 1, 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 B7
B: Aldo-keto reductase family 1, member B7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8724
Polymers72,3862
Non-polymers1,4872
Water11,836657
1
A: Aldo-keto reductase family 1, member B7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9362
Polymers36,1931
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Aldo-keto reductase family 1, member B7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9362
Polymers36,1931
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.859, 69.302, 87.946
Angle α, β, γ (deg.)90.00, 96.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Aldo-keto reductase family 1, member B7 / RCG28223 / isoform CRA_a


Mass: 36192.809 Da / Num. of mol.: 2 / Mutation: H269R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Akr1b7, rCG_28223 / Plasmid: pColdIV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5RJP0
#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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 657 / 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: 2.13 Å3/Da / Density % sol: 42.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 20% polyethylene glycol 4000, 2% 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 295K, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 3, 2010 / Details: Mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.87→30 Å / Num. all: 48259 / Num. obs: 46136 / % possible obs: 95.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 3.45 % / Rmerge(I) obs: 0.0374 / Net I/σ(I): 20.8
Reflection shellResolution: 1.87→1.94 Å / Redundancy: 2.86 % / Rmerge(I) obs: 0.1165 / Mean I/σ(I) obs: 5.4 / Num. unique all: 4159 / % possible all: 86.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3O3R

3o3r


Resolution: 1.87→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.45 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23172 2163 4.9 %RANDOM
Rwork0.16358 ---
obs0.16703 46136 87.43 %-
all-48259 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.456 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20.13 Å2
2--0.12 Å20 Å2
3----0.62 Å2
Refine analyzeLuzzati coordinate error obs: 0.208 Å
Refinement stepCycle: LAST / Resolution: 1.87→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5084 0 96 657 5837
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0225312
X-RAY DIFFRACTIONr_angle_refined_deg1.8691.9897199
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.035630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.73924.701234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54815965
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1681522
X-RAY DIFFRACTIONr_chiral_restr0.1330.2789
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213928
X-RAY DIFFRACTIONr_mcbond_it1.0381.53155
X-RAY DIFFRACTIONr_mcangle_it1.67425114
X-RAY DIFFRACTIONr_scbond_it2.82632157
X-RAY DIFFRACTIONr_scangle_it4.0994.52084
LS refinement shellResolution: 1.87→1.918 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 128 -
Rwork0.301 2412 -
obs-3581 69.13 %

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