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- PDB-2fje: adenosine-5-phosphosulfate reductase oxidized state -

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Basic information

Entry
Database: PDB / ID: 2fje
Titleadenosine-5-phosphosulfate reductase oxidized state
Components
  • adenylylsulfate reductase, subunit A
  • adenylylsulfate reductase, subunit B
KeywordsOXIDOREDUCTASE / APS reductase / sulfur cycle
Function / homology
Function and homology information


4 iron, 4 sulfur cluster binding / oxidoreductase activity / nucleotide binding / metal ion binding
Similarity search - Function
Signal recognition particle alu RNA binding heterodimer, srp9/1 / Adenylylsulphate reductase, beta subunit, C-terminal domain / Adenylylsulphate reductase, beta subunit / Adenylylsulphate reductase, alpha subunit / Adenylylsulphate reductase, beta subunit, C-terminal / APS reductase, beta subunit, C-terminal domain superfamily / Adenosine-5'-phosphosulfate reductase beta subunit / 4Fe-4S binding domain / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain / FAD-dependent oxidoreductase SdhA/FrdA/AprA ...Signal recognition particle alu RNA binding heterodimer, srp9/1 / Adenylylsulphate reductase, beta subunit, C-terminal domain / Adenylylsulphate reductase, beta subunit / Adenylylsulphate reductase, alpha subunit / Adenylylsulphate reductase, beta subunit, C-terminal / APS reductase, beta subunit, C-terminal domain superfamily / Adenosine-5'-phosphosulfate reductase beta subunit / 4Fe-4S binding domain / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain / FAD-dependent oxidoreductase SdhA/FrdA/AprA / Flavocytochrome C3; Chain A, domain 1 / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal / Fumarate reductase flavoprotein C-term / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / FAD-dependent oxidoreductase 2, FAD binding domain / FAD binding domain / 4Fe-4S binding domain / Alpha-Beta Plaits - #20 / Other non-globular / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / FAD/NAD(P)-binding domain / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / FAD/NAD(P)-binding domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / 3-Layer(bba) Sandwich / Special / FAD/NAD(P)-binding domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha-Beta Plaits / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / IRON/SULFUR CLUSTER / Adenylylsulfate reductase, subunit A (AprA) / Adenylylsulfate reductase, subunit B (AprB)
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsSchiffer, A. / Fritz, G. / Kroneck, P.M. / Ermler, U.
CitationJournal: Biochemistry / Year: 2006
Title: Reaction mechanism of the iron-sulfur flavoenzyme adenosine-5'-phosphosulfate reductase based on the structural characterization of different enzymatic states
Authors: Schiffer, A. / Fritz, G. / Kroneck, P.M. / Ermler, U.
History
DepositionJan 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: adenylylsulfate reductase, subunit A
C: adenylylsulfate reductase, subunit A
B: adenylylsulfate reductase, subunit B
D: adenylylsulfate reductase, subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,61210
Polymers180,6354
Non-polymers2,9786
Water20,0151111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28120 Å2
ΔGint-206 kcal/mol
Surface area46840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.600, 113.500, 193.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a heterotetramer present in the asymmetric unit

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Components

#1: Protein adenylylsulfate reductase, subunit A / aprA


Mass: 73359.695 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Archaeoglobus fulgidus (archaea) / References: UniProt: O28603, adenylyl-sulfate reductase
#2: Protein adenylylsulfate reductase, subunit B / aprB


Mass: 16957.650 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Archaeoglobus fulgidus (archaea) / References: UniProt: O28604, adenylyl-sulfate reductase
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1111 / Source method: isolated from a natural source / Formula: H2O

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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: 2.21 Å3/Da / Density % sol: 44.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 6 % PEG 4000, 0.1 M NaCl, 0.1 M NaAc pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 138616 / % possible obs: 92.6 % / Rmerge(I) obs: 0.038 / Χ2: 1.031
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.820.10918671.04537.8
1.82-1.840.07138630.73679
1.84-1.860.06441830.58984.1
1.86-1.890.06342850.61587.4
1.89-1.910.06542500.62585.8
1.91-1.940.05943360.6188.2
1.94-1.970.05443670.61488.4
1.97-20.05544940.70591.1
2-2.030.0545310.71191.1
2.03-2.060.04845590.72692.6
2.06-2.10.04946140.71993.2
2.1-2.130.04846610.72393.8
2.13-2.180.04747170.77895.8
2.18-2.220.04747030.8295.1
2.22-2.270.04747980.90696.3
2.27-2.320.04648540.98998.2
2.32-2.380.04548200.97897.3
2.38-2.440.04348841.00398.1
2.44-2.510.04248930.96998.4
2.51-2.60.04149481.11398.8
2.6-2.690.0449161.01998.9
2.69-2.80.03949721.17399.3
2.8-2.920.03749571.10699.5
2.92-3.080.03549901.22899.6
3.08-3.270.03549771.29299.6
3.27-3.520.03450131.46499.5
3.52-3.880.03450221.6499.4
3.88-4.430.03450301.62498.9
4.43-5.580.03250831.58598.7
5.58-300.03450291.4293.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→30 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.192 6400 4.3 %
Rwork0.166 --
obs-127075 85.4 %
Solvent computationBsol: 52.828 Å2
Displacement parametersBiso mean: 15.179 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---4.042 Å20 Å2
3---4.112 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12669 0 138 1111 13918
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2cof.parCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5cof.top

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