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- PDB-9b2g: Crystal structure of short chain dehydrogenase reductase 9 (short... -

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Basic information

Entry
Database: PDB / ID: 9b2g
TitleCrystal structure of short chain dehydrogenase reductase 9 (short chain dehydrogenase reductase 9C4) in complex with NADH
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
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Dehydrogenase/reductase SDR family member 9
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
B: Dehydrogenase/reductase SDR family member 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9094
Polymers70,5782
Non-polymers1,3312
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7070 Å2
ΔGint-38 kcal/mol
Surface area24810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.116, 74.205, 102.771
Angle α, β, γ (deg.)90.00, 133.12, 90.00
Int Tables number5
Space group name H-MC121

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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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dhrs9 / Plasmid: pet19b / Production host: Escherichia coli (E. coli)
References: UniProt: Q58NB6, 3(or 17)alpha-hydroxysteroid dehydrogenase, 3alpha(or 20beta)-hydroxysteroid dehydrogenase, all-trans-retinol dehydrogenase (NAD+)
#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 3.04 Å3/Da / Density % sol: 59.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.4 / Details: 15% Jeffamine SD-2001, 0.1 M Na citrate pH 5.4

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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: Nov 19, 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: 2→50 Å / Num. obs: 52809 / % possible obs: 99.3 % / Redundancy: 4.5 % / CC1/2: 0.999 / Rpim(I) all: 0.033 / Net I/σ(I): 10.5
Reflection shellResolution: 2→2.11 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2 / Num. unique obs: 7651 / CC1/2: 0.809 / Rpim(I) all: 0.426 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→40 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.952 / SU B: 20.458 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23844 2680 5.1 %RANDOM
Rwork0.20148 ---
obs0.20334 49599 98.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.779 Å2
Baniso -1Baniso -2Baniso -3
1-6.28 Å2-0 Å24.2 Å2
2---9.23 Å2-0 Å2
3----1.79 Å2
Refinement stepCycle: 1 / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4599 0 88 32 4719
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0134789
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154674
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.6396500
X-RAY DIFFRACTIONr_angle_other_deg1.2111.58510784
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9035595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.88622.5200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.81415833
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2531522
X-RAY DIFFRACTIONr_chiral_restr0.060.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025303
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021027
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8176.2812386
X-RAY DIFFRACTIONr_mcbond_other2.8146.2812385
X-RAY DIFFRACTIONr_mcangle_it4.1669.4272979
X-RAY DIFFRACTIONr_mcangle_other4.1679.4272980
X-RAY DIFFRACTIONr_scbond_it3.2396.7122403
X-RAY DIFFRACTIONr_scbond_other3.2396.7122404
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1519.9023522
X-RAY DIFFRACTIONr_long_range_B_refined6.60972.8365072
X-RAY DIFFRACTIONr_long_range_B_other6.6172.8375071
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 9222 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 205 -
Rwork0.386 3398 -
obs--92.2 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0806-0.8863-1.44152.04580.70181.8337-0.1653-0.1874-0.170.33360.08590.06210.28550.0960.07950.08460.00920.00530.01840.01660.017113.202-1.82731.628
21.8088-1.1128-1.52382.3090.87321.80130.0716-0.11440.2888-0.13570.0911-0.4129-0.17160.1688-0.16280.0413-0.01440.02270.02560.00280.115130.55.38212.745
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 304
2X-RAY DIFFRACTION2B22 - 304

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