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- PDB-6uhx: Crystal structure of YIR035C short chain dehydrogenases/reductase... -

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Basic information

Entry
Database: PDB / ID: 6uhx
TitleCrystal structure of YIR035C short chain dehydrogenases/reductase from Saccharomyces cerevisiae
ComponentsUncharacterized oxidoreductase YIR035C
KeywordsOXIDOREDUCTASE / CYTOPLASMIC PROTEIN / SHORT CHAIN DEHYDROGENASE / REDUCTASE
Function / homology
Function and homology information


: / oxidoreductase activity, acting on NAD(P)H, oxygen as acceptor / Oxidoreductases / cytoplasm
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Uncharacterized oxidoreductase YIR035C
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsStogios, P.J. / Skarina, T. / Chen, C. / Kagan, O. / Iakounine, A. / Savchenko, A.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)Industrial Biocatalysis Network Canada
CitationJournal: To Be Published
Title: Crystal structure of YIR035C short chain dehydrogenases/reductase from Saccharomyces cerevisiae
Authors: Chen, C.
History
DepositionSep 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized oxidoreductase YIR035C
B: Uncharacterized oxidoreductase YIR035C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5044
Polymers55,0172
Non-polymers1,4872
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-32 kcal/mol
Surface area19110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.545, 73.049, 67.800
Angle α, β, γ (deg.)90.000, 100.137, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Uncharacterized oxidoreductase YIR035C


Mass: 27508.494 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: YIR035C / Plasmid: p15Tv lic / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Magic / References: UniProt: P40579, Oxidoreductases
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.28 Å3/Da / Density % sol: 46.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M Bis-tris buffer, 5% iso-propanol, 2.4 M ammonium sulfate, 1/1600 chymotrypsin, 10 mM NADPH

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. obs: 12870 / % possible obs: 98.9 % / Redundancy: 4.4 % / Biso Wilson estimate: 47.42 Å2 / Rmerge(I) obs: 0.195 / Rpim(I) all: 0.103 / Net I/σ(I): 6.7
Reflection shellResolution: 2.75→2.8 Å / Rmerge(I) obs: 0.731 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 597 / CC1/2: 0.667 / Rpim(I) all: 0.406 / % possible all: 90.6

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Processing

Software
NameVersionClassification
PHENIX1.15_3448refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
Cootmodel building
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KZV

3kzv


Resolution: 2.75→29.64 Å / SU ML: 0.5369 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.9352
RfactorNum. reflection% reflection
Rfree0.3151 584 5 %
Rwork0.2351 --
obs0.239 11678 89.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 57.77 Å2
Refinement stepCycle: LAST / Resolution: 2.75→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3858 0 96 104 4058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00324030
X-RAY DIFFRACTIONf_angle_d0.69075480
X-RAY DIFFRACTIONf_chiral_restr0.0417631
X-RAY DIFFRACTIONf_plane_restr0.0027691
X-RAY DIFFRACTIONf_dihedral_angle_d20.7491468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-3.020.46481060.36912021X-RAY DIFFRACTION65.45
3.02-3.460.39911490.29762834X-RAY DIFFRACTION92.01
3.46-4.360.3221640.23143093X-RAY DIFFRACTION99.94
4.36-29.640.23661650.18363146X-RAY DIFFRACTION99.94
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)
10.92676542931-0.3826963137311.465014145436.14122662502-1.884374135038.272929580420.234404665954-0.926547627678-0.123274572127-0.2619767501230.280451204592-0.4301946724220.5431187242970.538250543494-0.3653708778210.317680573414-0.00079165263438-0.1076570678080.6998763468190.0730795151810.316669336314-2.9463333355716.1101725639-11.9817197598
27.69789306763-0.107664353134-1.896924473643.017961185910.4285930307572.228990403050.331838298315-1.185017284140.805082987119-0.184182137018-0.0617886098395-0.206850391566-0.7246780586810.73419611324-0.1921053853890.435429785848-0.080216088985-0.02990644045150.363279888529-0.08751713534960.364495678801-0.68156258204424.5318709939-14.6593775045
37.05996414119-1.766877578786.166082179952.30118426139-1.578277405099.12190376013-0.753913064888-1.14284791596-0.135699153909-0.001703410810970.6460181987750.131897617732-1.06023446224-1.28514297665-0.01310967857770.2922955014480.02739710485850.01370998088670.363091852775-0.02542633506130.30751327073-11.98562259115.4177255153-28.5324123248
44.575716669830.385914883649-0.1874355845581.904997070421.580979992882.74117140046-0.144752636041-0.2498048164370.101277047487-0.2247827985350.0214110678315-0.0139580179341-0.1882215184930.2977995241050.09988489297570.2686233231960.0226999265163-0.05778416920770.345971484870.07282128086190.293050021988-5.1561543925711.4404967332-30.4740898988
50.02837975841150.2467750830470.2727217565212.604742408350.6792339183066.099399150120.299533864033-0.444575443668-0.6042236868140.407285159543-0.1597878651390.3802861487660.273402929068-0.887669089969-0.1782293059880.342969270252-0.12636811212-0.04285262437790.4333478022110.05071509844290.328290455447-14.83693838269.56389695381-23.5003927653
69.461462953041.597856271141.414919771399.754682043592.234558961020.6958284993670.100573454023-1.497871038010.494267100557-0.3183442574730.1953877281581.32988691696-0.363502609321-0.207567318559-0.1938863710730.368031306921-0.16969296269-0.1031922899420.9777128481490.2084984934331.03384391763-28.79876136434.14830906014-21.9128265384
73.18184988338-0.104129692757-1.209233640470.9546520845731.756750681313.550975611760.279106118464-0.170086437968-0.8464126179-0.238694501722-0.2573500859470.230830510942-0.088851488615-0.0908736198221-0.05272983057150.702660496330.0196467448376-0.1280226358140.4906950424190.1572953934810.484589285303-5.869008276580.784209438038-16.8465461933
83.86262600619-1.7380962436-1.045989496535.603691103580.6764304782144.410438863630.3790845471730.9621038631870.02493390326260.186787003043-0.06595210590040.416933294255-0.2743553001-0.443431655094-0.2884010370750.3841535260070.1160580107910.04623908773020.610327521080.1169874289330.30591136388-15.509080501413.1736866646-63.8356352587
97.159366895720.5484619033322.36619133171.645035572850.7047763354294.335551225860.03229700889120.2118857716090.0934361822842-0.335319932554-0.0581035851977-0.0801673696352-0.196044765974-0.1072068519270.05581748456610.4114560826150.07355718356250.01300319196040.1972896953290.003458975075120.233701426454-10.130167575110.1919391452-45.5283403619
104.491578766913.53855933877-3.71636855035.10488253211-1.241085566024.203807399690.3593631742060.6437780531020.6224930852280.330221311259-0.0130672097002-0.160284377688-0.2627744697920.0802163970167-0.2392526175920.436903767565-0.0126327188501-0.06134467637610.4622366892950.01212893252960.319751945093-7.315551820473.83345820947-51.8674720254
116.51669479017-5.542332031864.04979308744.70165205865-3.772803611168.80443527688-0.1230042327490.0255591363828-0.126338221074-0.06564828743010.836741013873-1.1550051913-1.497470811850.513603470606-0.4615289058450.297472062356-0.0506741901520.1126200912640.670222066926-0.145837259290.68697823358212.10826293243.70833752769-49.9989735745
129.72816798618-0.160928856525-3.488465700931.728425721952.251713734814.198681990140.04700009637791.05393461898-0.5591695383770.113267978001-0.1611395376970.2339496334620.193027779276-0.7166898112620.1624118670170.454185825644-0.0705558985079-0.08593810481630.4383813349830.02299386349130.340340914647-11.3029604303-4.70469863375-54.8831315731
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 76 )
3X-RAY DIFFRACTION3chain 'A' and (resid 77 through 99 )
4X-RAY DIFFRACTION4chain 'A' and (resid 100 through 167 )
5X-RAY DIFFRACTION5chain 'A' and (resid 168 through 199 )
6X-RAY DIFFRACTION6chain 'A' and (resid 200 through 211 )
7X-RAY DIFFRACTION7chain 'A' and (resid 212 through 254 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 76 )
9X-RAY DIFFRACTION9chain 'B' and (resid 77 through 167 )
10X-RAY DIFFRACTION10chain 'B' and (resid 168 through 190 )
11X-RAY DIFFRACTION11chain 'B' and (resid 191 through 211 )
12X-RAY DIFFRACTION12chain 'B' and (resid 212 through 254 )

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