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- PDB-9b2f: Crystal structure of short chain dehydrogenase reductase 9 (short... -

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Basic information

Entry
Database: PDB / ID: 9b2f
TitleCrystal structure of short chain dehydrogenase reductase 9 (short chain dehydrogenase reductase 9C4) in complex with NAD+
ComponentsDehydrogenase/reductase SDR family member 9
KeywordsOXIDOREDUCTASE / short-chain dehydrogenase reductase / oxylipins / polyunsaturated fatty acids
Function / homology
Function and homology information


The canonical retinoid cycle in rods (twilight vision) / 9-cis-retinoic acid biosynthetic process / RA biosynthesis pathway / all-trans-retinol dehydrogenase (NAD+) / 3(or 17)alpha-hydroxysteroid dehydrogenase / androsterone dehydrogenase [NAD(P)+] activity / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase (NAD+) activity / testosterone dehydrogenase (NAD+) activity / progesterone metabolic process ...The canonical retinoid cycle in rods (twilight vision) / 9-cis-retinoic acid biosynthetic process / RA biosynthesis pathway / all-trans-retinol dehydrogenase (NAD+) / 3(or 17)alpha-hydroxysteroid dehydrogenase / androsterone dehydrogenase [NAD(P)+] activity / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase (NAD+) activity / testosterone dehydrogenase (NAD+) activity / progesterone metabolic process / alcohol dehydrogenase (NAD+) activity / all-trans-retinol dehydrogenase (NAD+) activity / androgen metabolic process / endoplasmic reticulum membrane
Similarity search - Function
short chain dehydrogenase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
MALONATE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Dehydrogenase/reductase SDR family member 9
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.662 Å
AuthorsPakhomova, S. / Belyaeva, O.V. / Boeglin, W.E. / Kedishvili, N.Y. / Brash, A.R. / Newcomer, M.E. / Popov, K.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)AR076924 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM134548 United States
CitationJournal: To Be Published
Title: The large substrate binding pocket of dehydrogenase reductase 9 underlies its ability to oxidize diverse pro-inflammatory and pro-resolving oxylipins.
Authors: Pakhomova, S. / Belyaeva, O.V. / Boeglin, W.E. / Kedishvili, N.Y. / Brash, A.R. / Newcomer, M.E. / Popov, K.M.
History
DepositionMar 15, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dehydrogenase/reductase SDR family member 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0553
Polymers35,2891
Non-polymers7652
Water2,576143
1
A: Dehydrogenase/reductase SDR family member 9
hetero molecules

A: Dehydrogenase/reductase SDR family member 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1096
Polymers70,5782
Non-polymers1,5314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area7330 Å2
ΔGint-36 kcal/mol
Surface area25090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.384, 103.045, 103.082
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-402-

MLI

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Components

#1: Protein Dehydrogenase/reductase SDR family member 9 / 3-alpha hydroxysteroid dehydrogenase / 3-alpha-HSD / Retinol dehydrogenase / Short-chain ...3-alpha hydroxysteroid dehydrogenase / 3-alpha-HSD / Retinol dehydrogenase / Short-chain dehydrogenase/reductase retSDR8


Mass: 35289.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dhrs9 / Plasmid: pet19b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q58NB6, 3(or 17)alpha-hydroxysteroid dehydrogenase, 3alpha(or 20beta)-hydroxysteroid dehydrogenase, all-trans-retinol dehydrogenase (NAD+)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.8 Å3/Da / Density % sol: 56.05 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 15% Jeffamine SD-2001, 0.1 M Na citrate pH 5.0, 0.1 M Na malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 9, 2021
RadiationMonochromator: cryogenically cooled single crystal SI(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.66→72.88 Å / Num. obs: 46581 / % possible obs: 99.2 % / Redundancy: 13 % / CC1/2: 0.999 / Rpim(I) all: 0.024 / Net I/σ(I): 13.5
Reflection shellResolution: 1.66→1.75 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 6403 / CC1/2: 0.764 / Rpim(I) all: 0.482

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.662→50.005 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.967 / WRfactor Rfree: 0.195 / WRfactor Rwork: 0.168 / SU B: 2.947 / SU ML: 0.085 / Average fsc free: 0.9226 / Average fsc work: 0.9263 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.076
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1931 968 2.079 %RANDOM
Rwork0.1661 45600 --
all0.167 ---
obs-46568 99.227 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 42.658 Å2
Baniso -1Baniso -2Baniso -3
1--2.535 Å2-0 Å20 Å2
2--4.69 Å20 Å2
3----2.155 Å2
Refinement stepCycle: LAST / Resolution: 1.662→50.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2299 0 51 143 2493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162371
X-RAY DIFFRACTIONr_angle_refined_deg1.8251.8243345
X-RAY DIFFRACTIONr_angle_other_deg0.61.7655480
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5155313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.722512
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.0151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.43610425
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.2671094
X-RAY DIFFRACTIONr_chiral_restr0.0860.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022824
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02531
X-RAY DIFFRACTIONr_nbd_refined0.2310.2452
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.21997
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21184
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21367
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2112
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0850.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1250.211
X-RAY DIFFRACTIONr_nbd_other0.1120.275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1070.232
X-RAY DIFFRACTIONr_mcbond_it3.7284.171211
X-RAY DIFFRACTIONr_mcbond_other3.7244.1691211
X-RAY DIFFRACTIONr_mcangle_it4.8797.4721516
X-RAY DIFFRACTIONr_mcangle_other4.8977.4721517
X-RAY DIFFRACTIONr_scbond_it5.2544.7521244
X-RAY DIFFRACTIONr_scbond_other5.2354.7471241
X-RAY DIFFRACTIONr_scangle_it8.0788.4091821
X-RAY DIFFRACTIONr_scangle_other8.0758.411822
X-RAY DIFFRACTIONr_lrange_it9.63641.8322710
X-RAY DIFFRACTIONr_lrange_other9.63240.1142673
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.662-1.7050.372780.3593034X-RAY DIFFRACTION90.0202
7.356-50.0050.186110.168597X-RAY DIFFRACTION99.8358

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