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- PDB-7rge: Crystal structure of phosphoadenylyl-sulfate (PAPS) reductase fro... -

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Basic information

Entry
Database: PDB / ID: 7rge
TitleCrystal structure of phosphoadenylyl-sulfate (PAPS) reductase from Candida auris, phosphate complex
Components3'-phosphoadenylylsulfate reductase
KeywordsOXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / sulfate reduction / PAPS reductase
Function / homology
Function and homology information


phosphoadenylyl-sulfate reductase (thioredoxin) / phosphoadenylyl-sulfate reductase (thioredoxin) activity / sulfate assimilation, phosphoadenylyl sulfate reduction by phosphoadenylyl-sulfate reductase (thioredoxin) / hydrogen sulfide biosynthetic process
Similarity search - Function
Phosphoadenosine phosphosulphate reductase CysH / Phosphoadenosine phosphosulphate/adenosine 5'-phosphosulphate reductase / Phosphoadenosine phosphosulphate reductase / Phosphoadenosine phosphosulfate reductase domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / 3'-phosphoadenylylsulfate reductase
Similarity search - Component
Biological speciesCandida auris (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsStogios, P.J. / Evdokimova, E. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: Crystal structure of phosphoadenylyl-sulfate (PAPS) reductase from Candida auris, phosphate complex
Authors: Stogios, P.J.
History
DepositionJul 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: 3'-phosphoadenylylsulfate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8774
Polymers27,5981
Non-polymers2793
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint-8 kcal/mol
Surface area10980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.508, 132.000, 44.617
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-440-

HOH

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Components

#1: Protein 3'-phosphoadenylylsulfate reductase / PAPS reductase / thioredoxin dependent / PAdoPS reductase


Mass: 27598.096 Da / Num. of mol.: 1 / Mutation: Q80A+E80A+K82A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida auris (fungus) / Gene: CAJCM15448_15210, CJI96_0004094 / Plasmid: pMCSG68SBPTEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Gold
References: UniProt: A0A510P1R8, phosphoadenylyl-sulfate reductase (thioredoxin)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.89 Å3/Da / Density % sol: 57.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M sodium chloride, 0.1 M HEPES, pH 7.5, 25% w/v PEG3350, 1 mM AMP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.38→30 Å / Num. obs: 13451 / % possible obs: 100 % / Redundancy: 6 % / Biso Wilson estimate: 57.32 Å2 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.027 / Net I/σ(I): 24.78
Reflection shellResolution: 2.38→2.42 Å / Rmerge(I) obs: 0.863 / Mean I/σ(I) obs: 1.06 / Num. unique obs: 662 / CC1/2: 0.875 / Rpim(I) all: 0.437

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OQ2

2oq2


Resolution: 2.38→28.26 Å / SU ML: 0.1867 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.5221
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2211 673 5.01 %RANDOM
Rwork0.1859 12768 --
obs0.1877 13441 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.8 Å2
Refinement stepCycle: LAST / Resolution: 2.38→28.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1632 0 17 105 1754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031687
X-RAY DIFFRACTIONf_angle_d0.58232295
X-RAY DIFFRACTIONf_chiral_restr0.0428259
X-RAY DIFFRACTIONf_plane_restr0.0048287
X-RAY DIFFRACTIONf_dihedral_angle_d22.4866608
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.560.28041310.24032490X-RAY DIFFRACTION99.7
2.56-2.820.27781330.23712526X-RAY DIFFRACTION99.96
2.82-3.220.25091330.22122529X-RAY DIFFRACTION100
3.23-4.060.24751350.1792560X-RAY DIFFRACTION100
4.06-28.260.18081410.16452663X-RAY DIFFRACTION99.93
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)
15.868406606621.47383127130.4420138399296.43734146425-3.083895120427.5430352575-0.4019632956831.36845710798-0.512091444424-1.526265991270.3927260180740.0594875479627-0.630555445015-1.02754207955-0.1179439666691.150027593970.223803361489-0.1191701056391.00487876662-0.1329569421610.65086834216-34.6607743314-10.8196545901-17.841876656
20.815960475223-1.99846174268-0.8466119195796.867670275254.843647561514.420229336850.07100296304480.2447219331890.102954251355-0.751106128099-0.190220889430.118351170823-0.910045150371-0.3472746764240.1065321154750.5930812173390.08803076323460.007317301381790.5252483182820.05265456768680.369162362821-30.948934591-19.0459781935-14.9419635554
31.978258459750.0952522134303-0.01116617514538.709385410152.081525472083.569819575490.16469089874-0.03228763180830.178410781325-0.188044931386-0.245923325083-0.105574735007-0.69273044416-0.02744431837760.05640438513410.4758927478440.0232100098447-0.02035554986160.480870265327-0.003999904504810.333872590236-33.6373040423-15.9280819447-4.7758464066
48.538789493286.071272750542.746871816836.613081452942.734089112425.049132445460.1081002131740.0454276706903-0.0686463571370.18724413522-0.2330804153940.4047660134470.174497464331-0.3131638091160.1251738487870.3209667503060.05120003740020.03395917229410.536791352368-0.0005360068521920.428325593605-46.8683099903-31.2951892251-8.96396942641
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 140 through 155 )140 - 155141 - 151
22chain 'A' and (resid 156 through 207 )156 - 207152 - 203
33chain 'A' and (resid 0 through 91 )0 - 911 - 92
44chain 'A' and (resid 92 through 139 )92 - 13993 - 140

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