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- PDB-3ln3: Crystal structure of Putative reductase (NP_038806.2) from MUS MU... -

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Basic information

Entry
Database: PDB / ID: 3ln3
TitleCrystal structure of Putative reductase (NP_038806.2) from MUS MUSCULUS at 1.18 A resolution
ComponentsDihydrodiol dehydrogenase
KeywordsOXIDOREDUCTASE / Putative reductase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


chlordecone reductase activity / steroid dehydrogenase activity / cellular response to jasmonic acid stimulus / androsterone dehydrogenase activity / ketosteroid monooxygenase activity / aldo-keto reductase (NADPH) activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / daunorubicin metabolic process / doxorubicin metabolic process / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor ...chlordecone reductase activity / steroid dehydrogenase activity / cellular response to jasmonic acid stimulus / androsterone dehydrogenase activity / ketosteroid monooxygenase activity / aldo-keto reductase (NADPH) activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / daunorubicin metabolic process / doxorubicin metabolic process / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / retinal dehydrogenase activity / aldose reductase (NADPH) activity / steroid metabolic process / xenobiotic metabolic process / oxidoreductase activity / cytosol
Similarity search - Function
Aldo-keto reductase family 1 member C / 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 1 member C / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Dihydrodiol dehydrogenase / Aldo-keto reductase family 1 member C13
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.18 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative reductase (NP_038806.2) from MUS MUSCULUS at 1.18 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydrodiol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2396
Polymers38,1701
Non-polymers1,0705
Water7,116395
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Dihydrodiol dehydrogenase
hetero molecules

A: Dihydrodiol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,47912
Polymers76,3392
Non-polymers2,14010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5650 Å2
ΔGint-104 kcal/mol
Surface area26870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.506, 47.206, 47.100
Angle α, β, γ (deg.)90.000, 94.980, 90.000
Int Tables number5
Space group name H-MC121
DetailsCRYSTAL PACKING ANALYSIS SUPPORTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIC FORM IN SOLUTION.

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Components

#1: Protein Dihydrodiol dehydrogenase / Putative reductase


Mass: 38169.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Akr1c13, ddh / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q54A37, UniProt: Q8VC28*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O
Sequence details1.THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED ...1.THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. 2.THE PROTEIN WAS REDUCTIVELY METHYLATED PRIOR TO CRYSTALLIZATION.

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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: 2.29 Å3/Da / Density % sol: 46.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 2.4000M ammonium sulfate, 0.1M TRIS pH 8.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97931
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 5, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.18→28.895 Å / Num. obs: 110769 / % possible obs: 95 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 7.922 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 6.23
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.18-1.220.4571.5211671420367.4
1.22-1.270.4031.7332252171994.6
1.27-1.330.3282.1344832241997.4
1.33-1.40.2642.6337062178098.4
1.4-1.490.1973.4350702252899.1
1.49-1.60.1364.7330412107199.3
1.6-1.760.16.3348822206099.1
1.76-2.020.0669.1356742239398.7
2.02-2.540.04613348362158398.2
2.54-28.8950.03716.6354752150496.2

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.18→28.895 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.973 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 1.046 / SU ML: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.033
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3.SULFATE (SO4) FROM THE CRYSTALLIZATION SOLUTION HAS BEEN MODELED IN THE SOLVENT STRUCTURE. 4.ENDOGENOUS NICOTINAMIDE ADENINE DINUCLEOTIDE (NAD), WHICH IS THE EXPECTED COFACTOR FOR THIS PROTEIN, HAS BEEN MODELED AT THE PUTATIVE ACTIVE SITE. THE NAD SHOWS SOME DISORDER IN THE STRUCTURE. 5.(4R)-2-METHYLPENTANE-2,4-DIOL (MRD), WHICH MAY BE A SUBSTRATE MIMIC, HAS BEEN MODELED IN THE PUTATIVE ACTIVE SITE BASED ON THE ELECTRON DENSITY. HOWEVER, IT IS POSSIBLE THAT THIS MAY BE SOME OTHER COMPOUND. 6.THE PROTEIN WAS SUBJECTED TO REDUCTIVE METHYLATION PRIOR TO CRYSTALLIZATION. LYSINE 84 APPEARS TO HAVE BEEN PROTECTED FROM REDUCTIVE METHYLATION AND WAS MODELED AS LYSINE. ALL OTHER LYSINES HAVE BEEN MODELED AS N-DIMETHYL-LYSINE (MLY).
RfactorNum. reflection% reflectionSelection details
Rfree0.156 5543 5 %RANDOM
Rwork0.131 ---
obs0.132 110769 97.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 53.39 Å2 / Biso mean: 12.405 Å2 / Biso min: 3.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0.21 Å2
2--0.39 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.18→28.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2799 0 67 405 3271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222960
X-RAY DIFFRACTIONr_bond_other_d0.0010.022016
X-RAY DIFFRACTIONr_angle_refined_deg1.8272.0364081
X-RAY DIFFRACTIONr_angle_other_deg0.99234980
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4675382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1724.697132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81215.272569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2051516
X-RAY DIFFRACTIONr_chiral_restr0.20.2473
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213205
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02553
X-RAY DIFFRACTIONr_mcbond_it1.75321708
X-RAY DIFFRACTIONr_mcbond_other0.8132672
X-RAY DIFFRACTIONr_mcangle_it2.46632811
X-RAY DIFFRACTIONr_scbond_it2.53321252
X-RAY DIFFRACTIONr_scangle_it3.6531238
X-RAY DIFFRACTIONr_rigid_bond_restr1.36534976
X-RAY DIFFRACTIONr_sphericity_free7.2623405
X-RAY DIFFRACTIONr_sphericity_bonded2.97934882
LS refinement shellResolution: 1.18→1.211 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 312 -
Rwork0.227 6249 -
all-6561 -
obs--78.52 %

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