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- PDB-4gac: High resolution structure of mouse aldehyde reductase (AKR1a4) in... -

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Basic information

Entry
Database: PDB / ID: 4gac
TitleHigh resolution structure of mouse aldehyde reductase (AKR1a4) in its apo-form
ComponentsAlcohol dehydrogenase [NADP(+)]
KeywordsOXIDOREDUCTASE / TIM barrel / aldheyde reductase akr1a4 / SMAR1
Function / homology
Function and homology information


mevaldate reductase (NADPH) / : / Formation of xylulose-5-phosphate / glucuronate reductase / glucuronolactone reductase / glucuronolactone reductase activity / D-glucuronate catabolic process / Glutathione conjugation / alcohol dehydrogenase (NADP+) / aldehyde catabolic process ...mevaldate reductase (NADPH) / : / Formation of xylulose-5-phosphate / glucuronate reductase / glucuronolactone reductase / glucuronolactone reductase activity / D-glucuronate catabolic process / Glutathione conjugation / alcohol dehydrogenase (NADP+) / aldehyde catabolic process / alcohol dehydrogenase (NADP+) activity / cellular detoxification of aldehyde / L-glucuronate reductase activity / D/L-glyceraldehyde reductase / L-ascorbic acid biosynthetic process / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / daunorubicin metabolic process / doxorubicin metabolic process / aldose reductase (NADPH) activity / oxidoreductase activity / apical plasma membrane / 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
CITRATE ANION / Aldo-keto reductase family 1 member A1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsFaucher, F. / Jia, Z.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: High-resolution structure of AKR1a4 in the apo form and its interaction with ligands.
Authors: Faucher, F. / Jia, Z.
History
DepositionJul 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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: Alcohol dehydrogenase [NADP(+)]
B: Alcohol dehydrogenase [NADP(+)]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5146
Polymers73,0112
Non-polymers5024
Water17,853991
1
A: Alcohol dehydrogenase [NADP(+)]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7573
Polymers36,5061
Non-polymers2512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alcohol dehydrogenase [NADP(+)]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7573
Polymers36,5061
Non-polymers2512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.940, 92.620, 70.100
Angle α, β, γ (deg.)90.000, 106.160, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alcohol dehydrogenase [NADP(+)] / Aldehyde reductase / Aldo-keto reductase family 1 member A1


Mass: 36505.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Akr1a1, Akr1a4 / Plasmid: pGEXT4T3-AKR1a4 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 DE3 / References: UniProt: Q9JII6, alcohol dehydrogenase (NADP+)
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 991 / 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: 2.43 Å3/Da / Density % sol: 49.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 26% PEG-4000, 0.1 M NaCitrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 15, 2010
RadiationMonochromator: Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.64→19.733 Å / Num. all: 85488 / Num. obs: 84168 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.96 % / Biso Wilson estimate: 18.223 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 19.7
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.64-1.680.1448182236163197.7
1.68-1.730.12710.28217666114199.4
1.73-1.780.10811.55213635956199.3
1.78-1.830.09313.07207595738199.3
1.83-1.890.08214.43202885582199.4
1.89-1.960.07316.13198185396198.9
1.96-2.030.06518.07191075204198.8
2.03-2.120.0619.73182504965198.5
2.12-2.210.05421.34173244744198.3
2.21-2.320.05322.47166994567198.2
2.32-2.440.04723.9157694321198.2
2.44-2.590.04524.97148944092197.2
2.59-2.770.04326.18140213840198.3
2.77-2.990.03827.69132313615198
2.99-3.280.03529.38121853300198.6
3.28-3.670.03230.94111043017197.9
3.67-4.230.02932.1297282640198.7
4.23-5.190.02632.7984312274198.4
5.19-7.330.02731.5164951751198.7
7.33-19.7330.02531.573045889188.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
Blu-Iceicedata collection
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HE8
Resolution: 1.64→19.733 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.9099 / SU ML: 0.17 / σ(F): 2 / Phase error: 16.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1784 4209 5 %RANDOM
Rwork0.148 ---
obs0.1495 84166 98.58 %-
all-84166 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.493 Å2 / ksol: 0.362 e/Å3
Displacement parametersBiso max: 62.76 Å2 / Biso mean: 13.2931 Å2 / Biso min: 2.07 Å2
Baniso -1Baniso -2Baniso -3
1-2.0855 Å2-0 Å21.0044 Å2
2---0.832 Å20 Å2
3----1.2535 Å2
Refinement stepCycle: LAST / Resolution: 1.64→19.733 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4997 0 34 991 6022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075327
X-RAY DIFFRACTIONf_angle_d1.1197282
X-RAY DIFFRACTIONf_chiral_restr0.075796
X-RAY DIFFRACTIONf_plane_restr0.007953
X-RAY DIFFRACTIONf_dihedral_angle_d13.7542020
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.64-1.65860.25821370.2032596273396
1.6586-1.67820.23721420.17772703284599
1.6782-1.69860.21211380.1652626276499
1.6986-1.72010.20131430.157627022845100
1.7201-1.74270.20551400.164626622802100
1.7427-1.76660.19361400.15542664280499
1.7666-1.79180.22261420.15492707284999
1.7918-1.81850.18731400.14692646278699
1.8185-1.84690.19721410.14522695283699
1.8469-1.87720.18551410.144126652806100
1.8772-1.90950.20051410.14232688282999
1.9095-1.94420.1781410.1472668280999
1.9442-1.98160.18211400.14862668280899
1.9816-2.0220.19211410.15192679282099
2.022-2.06590.19621390.14872651279099
2.0659-2.11390.18781400.14652658279898
2.1139-2.16670.15531390.14012625276499
2.1667-2.22520.19711410.14592678281998
2.2252-2.29060.16931380.14982640277898
2.2906-2.36440.18151420.14732690283298
2.3644-2.44880.18181380.14392623276198
2.4488-2.54660.1571390.14942631277098
2.5466-2.66230.17641400.15042665280598
2.6623-2.80230.17191400.1492663280398
2.8023-2.97730.15281400.14792656279698
2.9773-3.20630.17871400.14472674281499
3.2063-3.52730.17961410.14152673281498
3.5273-4.03390.14241420.13222689283199
4.0339-5.0680.14891400.12332673281399
5.068-19.73440.19041430.18182699284297

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