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- PDB-5jgy: Crystal structure of maize AKR4C13 in P21 space group -

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Basic information

Entry
Database: PDB / ID: 5jgy
TitleCrystal structure of maize AKR4C13 in P21 space group
ComponentsAldose reductase, AKR4C13
KeywordsOXIDOREDUCTASE / aldo-keto reductase superfamily / AKR4C subfamily
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
Aldo-keto reductase family 4C / 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 4C / 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
Chem-6KB / Aldose reductase
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.45 Å
AuthorsSantos, M.L. / Giuseppe, P.O. / Kiyota, E. / Sousa, S.M. / Schmelz, E.A. / Yunes, J.A. / Koch, K.E. / Murakami, M.T. / Aparicio, R.
CitationJournal: To Be Published
Title: Crystal structure of maize AKR4C13 in P21 space group
Authors: Sousa, S.M. / Giuseppe, P.O. / Murakami, M.T. / Kiyota, E. / Santos, M.L. / Aparicio, R. / Schmelz, E.A. / Yunes, J.A. / Koch, K.E.
History
DepositionApr 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2017Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aldose reductase, AKR4C13
B: Aldose reductase, AKR4C13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,66915
Polymers73,5362
Non-polymers2,13413
Water12,845713
1
A: Aldose reductase, AKR4C13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7426
Polymers36,7681
Non-polymers9745
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Aldose reductase, AKR4C13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9289
Polymers36,7681
Non-polymers1,1608
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.750, 115.301, 56.466
Angle α, β, γ (deg.)90.000, 104.280, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Aldose reductase, AKR4C13 / Uncharacterized protein


Mass: 36767.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: AR3 / Production host: Escherichia coli (E. coli) / References: UniProt: E9JVD4
#2: Chemical ChemComp-6KB / 4-{[(2R,3R,4S,5R)-5-({[(R)-{[(R)-{[(2R,3R,4R,5R)-5-(6-amino-9H-purin-9-yl)-3-hydroxy-4-(phosphonooxy)tetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-3,4-dihydroxytetrahydrofuran-2-yl]oxy}butanoic acid (non-preferred name)


Mass: 725.385 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H30N5O19P3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 713 / 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: 2.31 Å3/Da / Density % sol: 46.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 15% (w/v) PEG 1500 and 0.1 M SPG buffer pH 4.5 added by 0.01 M of beta-NAD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.45→57.65 Å / Num. obs: 230943 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 21.264 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 11.37
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.45-1.540.6441.4198.6
1.54-1.640.3922.26199.1
1.64-1.770.233.75199
1.77-1.940.1286.44199
1.94-2.170.06811.34198.9
2.17-2.510.04217.46198.7
2.51-3.070.02724.7198.6
3.07-4.320.01737.63198
4.320.01643.36195.1

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.15data extraction
BALBESphasing
RefinementResolution: 1.45→57.65 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.152 / WRfactor Rwork: 0.1194 / FOM work R set: 0.8936 / SU B: 2.515 / SU ML: 0.041 / SU R Cruickshank DPI: 0.0592 / SU Rfree: 0.0552 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1627 5866 5 %RANDOM
Rwork0.1261 ---
obs0.1279 112065 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.15 Å2 / Biso mean: 18.981 Å2 / Biso min: 7.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å2-0 Å20.02 Å2
2---0.35 Å2-0 Å2
3----0.07 Å2
Refinement stepCycle: final / Resolution: 1.45→57.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4874 0 228 713 5815
Biso mean--15.62 32.41 -
Num. residues----617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195359
X-RAY DIFFRACTIONr_bond_other_d0.0010.025078
X-RAY DIFFRACTIONr_angle_refined_deg1.5972.0037271
X-RAY DIFFRACTIONr_angle_other_deg0.785311736
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.735642
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65323.66235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.85415913
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6011540
X-RAY DIFFRACTIONr_chiral_restr0.0760.2777
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215873
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021179
X-RAY DIFFRACTIONr_mcbond_it1.6931.582535
X-RAY DIFFRACTIONr_mcbond_other1.6921.5792534
X-RAY DIFFRACTIONr_mcangle_it2.1272.3833185
X-RAY DIFFRACTIONr_rigid_bond_restr2.383310437
X-RAY DIFFRACTIONr_sphericity_free33.0485190
X-RAY DIFFRACTIONr_sphericity_bonded10.926510834
LS refinement shellResolution: 1.448→1.485 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 428 -
Rwork0.26 8200 -
all-8628 -
obs--99.21 %

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