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- PDB-3o3r: Crystal Structure of AKR1B14 in complex with NADP -

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Basic information

Entry
Database: PDB / ID: 3o3r
TitleCrystal Structure of AKR1B14 in complex with NADP
ComponentsAldo-keto reductase family 1, member B7
KeywordsOXIDOREDUCTASE / Aldose reductase like protein / 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 / molecular replacement / Resolution: 1.86 Å
AuthorsSundaram, K. / Dhagat, U. / El-Kabbani, O.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2011
Title: Structure of rat aldose reductase-like protein AKR1B14 holoenzyme: Probing the role of His269 in coenzyme binding by site-directed mutagenesis
Authors: Sundaram, K. / Dhagat, U. / Endo, S. / Chung, R. / Matsunaga, T. / Hara, A. / El-Kabbani, O.
History
DepositionJul 26, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)73,8344
Polymers72,3482
Non-polymers1,4872
Water11,440635
1
A: Aldo-keto reductase family 1, member B7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9172
Polymers36,1741
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)36,9172
Polymers36,1741
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.666, 69.146, 87.833
Angle α, β, γ (deg.)90.000, 96.470, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Aldo-keto reductase family 1, member B7 / Aldo - Keto Reductase like protein


Mass: 36173.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pCold IV / 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.: 635 / 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: 2.11 Å3/Da / Density % sol: 41.79 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 20% polyethylene glycol 4000, 10% 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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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: Jan 7, 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: 1.86→30 Å / Num. all: 50520 / Num. obs: 49358 / % possible obs: 97.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 3.48 % / Rmerge(I) obs: 0.0477 / Net I/σ(I): 13.5
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 3.02 % / Rmerge(I) obs: 0.2796 / Mean I/σ(I) obs: 2.3 / Num. unique all: 4018 / % possible all: 90.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PWL
Resolution: 1.86→28.5 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2536 / WRfactor Rwork: 0.1892 / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.8216 / SU B: 3.85 / SU ML: 0.116 / SU R Cruickshank DPI: 0.1742 / SU Rfree: 0.1656 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2489 2432 4.9 %RANDOM
Rwork0.1851 ---
obs0.1883 49358 97.71 %-
all-50520 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 63.21 Å2 / Biso mean: 27.0707 Å2 / Biso min: 8.06 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20 Å20.68 Å2
2--0.11 Å20 Å2
3----1.14 Å2
Refine analyzeLuzzati coordinate error obs: 0.208 Å
Refinement stepCycle: LAST / Resolution: 1.86→28.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5082 0 96 635 5813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0225310
X-RAY DIFFRACTIONr_angle_refined_deg1.9331.9867197
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1945630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.57324.786234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35115961
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.271520
X-RAY DIFFRACTIONr_chiral_restr0.1310.2789
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213922
X-RAY DIFFRACTIONr_mcbond_it1.1561.53153
X-RAY DIFFRACTIONr_mcangle_it1.87225110
X-RAY DIFFRACTIONr_scbond_it3.07132157
X-RAY DIFFRACTIONr_scangle_it4.5134.52086
LS refinement shellResolution: 1.862→1.93 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.531 156 -
Rwork0.428 3119 -
all-3275 -
obs-3640 89.14 %

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