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- PDB-7n09: Structural basis for branched substrate selectivity in a ketoredu... -

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Basic information

Entry
Database: PDB / ID: 7n09
TitleStructural basis for branched substrate selectivity in a ketoreductase from Ascaris suum
Components3-hydroxyacyl-CoA dehydrogenase type-2
KeywordsOXIDOREDUCTASE / ketoreductase
Function / homology
Function and homology information


estradiol 17-beta-dehydrogenase [NAD(P)+] activity / estrogen metabolic process / androgen metabolic process / fatty acid metabolic process / nucleotide binding / mitochondrion
Similarity search - Function
short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 3-hydroxyacyl-CoA dehydrogenase type-2
Similarity search - Component
Biological speciesAscaris suum (pig roundworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDong, H. / Chang, M.C.Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1413862 United States
CitationJournal: Acs Catalysis / Year: 2021
Title: Structural Basis for Branched Substrate Selectivity in a Ketoreductase from Ascaris suum
Authors: Dong, H. / Chang, M.C.Y.
History
DepositionMay 25, 2021Deposition site: RCSB / Processing site: RCSB
SupersessionAug 11, 2021ID: 6U5I
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-hydroxyacyl-CoA dehydrogenase type-2
B: 3-hydroxyacyl-CoA dehydrogenase type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0594
Polymers58,7322
Non-polymers1,3272
Water6,756375
1
A: 3-hydroxyacyl-CoA dehydrogenase type-2
B: 3-hydroxyacyl-CoA dehydrogenase type-2
hetero molecules

A: 3-hydroxyacyl-CoA dehydrogenase type-2
B: 3-hydroxyacyl-CoA dehydrogenase type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,1178
Polymers117,4634
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area20200 Å2
ΔGint-139 kcal/mol
Surface area31660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.542, 54.942, 89.270
Angle α, β, γ (deg.)90.000, 131.039, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-548-

HOH

21A-587-

HOH

31B-550-

HOH

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Components

#1: Protein 3-hydroxyacyl-CoA dehydrogenase type-2


Mass: 29365.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ascaris suum (pig roundworm) / Plasmid: pET23a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F1L0H2
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.02 Å3/Da / Density % sol: 39.23 %
Crystal growTemperature: 290 K / Method: evaporation / pH: 6.5
Details: 35% PEG550 MME, 144 mM potassium sodium tartrate, 100 mM MES, pH6.5 2 M sodium malonate, pH 6.5
PH range: 6.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.3.110.73
SYNCHROTRONALS 8.3.122.5
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 5, 2017
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.731
22.51
ReflectionResolution: 1.75→67.33 Å / Num. obs: 84379 / % possible obs: 89.4 % / Redundancy: 2 % / Biso Wilson estimate: 31.22 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.5
Reflection shellResolution: 1.75→1.81 Å / Num. unique obs: 4507 / CC1/2: 0.196

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
BALBESphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1e6w

1e6w


Resolution: 2→67.33 Å / SU ML: 0.2299 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.8638 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.22 2821 4.54 %
Rwork0.177 59347 -
obs0.1789 62168 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.99 Å2
Refinement stepCycle: LAST / Resolution: 2→67.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3798 0 88 375 4261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01593952
X-RAY DIFFRACTIONf_angle_d1.10455360
X-RAY DIFFRACTIONf_chiral_restr0.57624
X-RAY DIFFRACTIONf_plane_restr0.0077688
X-RAY DIFFRACTIONf_dihedral_angle_d15.40251400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.31171440.29332992X-RAY DIFFRACTION97.91
2.03-2.070.38531480.2812906X-RAY DIFFRACTION100
2.07-2.110.30591430.24723004X-RAY DIFFRACTION99.9
2.11-2.150.30281490.2382894X-RAY DIFFRACTION99.8
2.15-2.20.23391420.22313019X-RAY DIFFRACTION99.91
2.2-2.250.23971010.21722994X-RAY DIFFRACTION100
2.25-2.310.23271130.21132980X-RAY DIFFRACTION99.74
2.31-2.370.25211100.20753054X-RAY DIFFRACTION99.87
2.37-2.440.25561170.2022941X-RAY DIFFRACTION100
2.44-2.520.26921210.18923015X-RAY DIFFRACTION99.9
2.52-2.610.26511540.19812986X-RAY DIFFRACTION99.94
2.61-2.710.19491360.20492936X-RAY DIFFRACTION100
2.71-2.840.2251810.19022897X-RAY DIFFRACTION99.68
2.84-2.990.27981550.19372958X-RAY DIFFRACTION100
2.99-3.170.24321520.18943015X-RAY DIFFRACTION99.84
3.17-3.420.19391130.17762947X-RAY DIFFRACTION99.84
3.42-3.760.19781830.15632917X-RAY DIFFRACTION99.87
3.76-4.310.1941430.14552987X-RAY DIFFRACTION99.97
4.31-5.430.18071880.12882926X-RAY DIFFRACTION99.87
5.43-67.330.16811280.13852979X-RAY DIFFRACTION99.68

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