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- PDB-2o8v: PAPS reductase in a covalent complex with thioredoxin C35A -

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Basic information

Entry
Database: PDB / ID: 2o8v
TitlePAPS reductase in a covalent complex with thioredoxin C35A
Components
  • Phosphoadenosine phosphosulfate reductase
  • Thioredoxin 1
KeywordsOXIDOREDUCTASE / Disulfide crosslinked complex
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) / glycerol ether metabolic process / hydrogen sulfide biosynthetic process / sulfur compound metabolic process / Oxidoreductases / DNA polymerase processivity factor activity / protein-disulfide reductase activity / cell redox homeostasis ...phosphoadenylyl-sulfate reductase (thioredoxin) / phosphoadenylyl-sulfate reductase (thioredoxin) activity / sulfate assimilation, phosphoadenylyl sulfate reduction by phosphoadenylyl-sulfate reductase (thioredoxin) / glycerol ether metabolic process / hydrogen sulfide biosynthetic process / sulfur compound metabolic process / Oxidoreductases / DNA polymerase processivity factor activity / protein-disulfide reductase activity / cell redox homeostasis / cytoplasm / cytosol
Similarity search - Function
Phosphoadenosine phosphosulphate reductase CysH / Phosphoadenosine phosphosulphate/adenosine 5'-phosphosulphate reductase / Phosphoadenosine phosphosulphate reductase / Phosphoadenosine phosphosulfate reductase family / Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / HUPs / Thioredoxin domain profile. ...Phosphoadenosine phosphosulphate reductase CysH / Phosphoadenosine phosphosulphate/adenosine 5'-phosphosulphate reductase / Phosphoadenosine phosphosulphate reductase / Phosphoadenosine phosphosulfate reductase family / Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / HUPs / Thioredoxin domain profile. / Thioredoxin domain / Rossmann-like alpha/beta/alpha sandwich fold / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thioredoxin 1 / Phosphoadenosine 5'-phosphosulfate reductase / Thioredoxin 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsChartron, J. / Shiau, C. / Stout, C.D. / Carroll, K.S.
CitationJournal: Biochemistry / Year: 2007
Title: 3'-Phosphoadenosine-5'-phosphosulfate Reductase in Complex with Thioredoxin: A Structural Snapshot in the Catalytic Cycle.
Authors: Chartron, J. / Shiau, C. / Stout, C.D. / Carroll, K.S.
History
DepositionDec 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 30, 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: Phosphoadenosine phosphosulfate reductase
B: Thioredoxin 1


Theoretical massNumber of molelcules
Total (without water)42,9092
Polymers42,9092
Non-polymers00
Water00
1
A: Phosphoadenosine phosphosulfate reductase
B: Thioredoxin 1

A: Phosphoadenosine phosphosulfate reductase
B: Thioredoxin 1


Theoretical massNumber of molelcules
Total (without water)85,8174
Polymers85,8174
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-11 kcal/mol
Surface area16910 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)40.932, 111.153, 153.434
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe second part of the biological assembly is generate by the two fold axis: -x, y, -z+1/2

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Components

#1: Protein Phosphoadenosine phosphosulfate reductase / PAPS reductase / thioredoxin dependent / PAdoPS reductase / 3'- phosphoadenylylsulfate reductase / ...PAPS reductase / thioredoxin dependent / PAdoPS reductase / 3'- phosphoadenylylsulfate reductase / PAPS sulfotransferase


Mass: 29081.924 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cysH / Plasmid: pET24b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE2)gold
References: UniProt: P17854, phosphoadenylyl-sulfate reductase (thioredoxin)
#2: Protein Thioredoxin 1


Mass: 13826.686 Da / Num. of mol.: 1 / Fragment: residues 37-144 / Mutation: C35A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trxA / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE2)gold
References: UniProt: Q1R4F8, UniProt: P0AA25*PLUS, Oxidoreductases

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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: 2.03 Å3/Da / Density % sol: 39.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 10% PEG3400, 0.2M Potassium dihydrogen phosphate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.9794
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 17, 2006
RadiationMonochromator: Double crystal, parallel, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3→27.789 Å / Num. all: 7334 / Num. obs: 7334 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 79.8 Å2 / Rmerge(I) obs: 0.137 / Rsym value: 0.137 / Net I/σ(I): 4.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3-3.084.80.4851.425285250.485100
3.08-3.164.90.4191.625695290.419100
3.16-3.254.80.34223144840.34100
3.25-3.354.80.2982.324195040.29899.9
3.35-3.464.70.2452.923014860.245100
3.46-3.594.60.2183.120344410.21899.8
3.59-3.724.70.1853.822094690.185100
3.72-3.874.70.1664.419554180.16699.9
3.87-4.054.70.1514.719634210.151100
4.05-4.244.50.1255.418034000.125100
4.24-4.474.60.1126.217483800.11299.8
4.47-4.744.40.1036.415123450.10399.6
4.74-5.074.50.0976.716003530.09799.5
5.07-5.484.40.0996.813863150.09999.2
5.48-64.40.1086.113093000.10899.9
6-6.714.30.1086.311502690.108100
6.71-7.7540.0877.69492370.08799
7.75-9.493.90.05610.37772000.05697.5
9.49-13.424.40.06397371680.06398.9
13.42-27.793.50.0638.2312900.06388.5

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3.18 Å27.79 Å
Translation3.18 Å27.79 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
CNS1.1refinement
PDB_EXTRACT2data extraction
Blu-Icedata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SUR, PDB ENTRY 2TRX

1sur

2trx


Resolution: 3→27.79 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 1452248.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: BUSTER used for initial rounds of refinement and completing missing part of structure. CNS used for final refinements.
RfactorNum. reflection% reflectionSelection details
Rfree0.307 369 5 %RANDOM
Rwork0.297 ---
all0.298 7319 --
obs0.298 7319 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.274 Å2 / ksol: 0.382 e/Å3
Displacement parametersBiso mean: 55.9 Å2
Baniso -1Baniso -2Baniso -3
1--21.13 Å20 Å20 Å2
2---8.96 Å20 Å2
3---30.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.5 Å
Luzzati d res low-5 Å
Luzzati sigma a0.73 Å0.66 Å
Refinement stepCycle: LAST / Resolution: 3→27.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2672 0 0 0 2672
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d1.06
X-RAY DIFFRACTIONc_mcbond_it1.121.5
X-RAY DIFFRACTIONc_mcangle_it2.012
X-RAY DIFFRACTIONc_scbond_it1.222
X-RAY DIFFRACTIONc_scangle_it2.032.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.056 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.419 56 4.7 %
Rwork0.386 1129 -
obs-1185 99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2

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