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- PDB-1j70: CRYSTAL STRUCTURE OF YEAST ATP SULFURYLASE -

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Basic information

Entry
Database: PDB / ID: 1j70
TitleCRYSTAL STRUCTURE OF YEAST ATP SULFURYLASE
ComponentsATP SULPHURYLASE
KeywordsTRANSFERASE / nucleotide binding fold and kinase fold
Function / homology
Function and homology information


: / sulfur amino acid metabolic process / sulfate adenylyltransferase / sulfate adenylyltransferase (ATP) activity / hydrogen sulfide biosynthetic process / mitochondrion / ATP binding / cytoplasm
Similarity search - Function
Sulfate adenylyltransferase / : / Sulfate adenylyltransferase / Sulfate adenylyltransferase / Sulphate adenylyltransferase / Sulphate adenylyltransferase catalytic domain / ATP-sulfurylase / ATP-sulfurylase PUA-like domain / PUA-like domain / PUA-like superfamily ...Sulfate adenylyltransferase / : / Sulfate adenylyltransferase / Sulfate adenylyltransferase / Sulphate adenylyltransferase / Sulphate adenylyltransferase catalytic domain / ATP-sulfurylase / ATP-sulfurylase PUA-like domain / PUA-like domain / PUA-like superfamily / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / P-loop containing nucleotide triphosphate hydrolases / Roll / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Sulfate adenylyltransferase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsLalor, D.J. / Schnyder, T. / Saridakis, V. / Pilloff, D.E. / Dong, A. / Tang, H. / Leyh, T.S. / Pai, E.F.
CitationJournal: Protein Eng. / Year: 2003
Title: Structural and functional analysis of a truncated form of Saccharomyces cerevisiae ATP sulfurylase: C-terminal domain essential for oligomer formation but not for activity.
Authors: Lalor, D.J. / Schnyder, T. / Saridakis, V. / Pilloff, D.E. / Dong, A. / Tang, H. / Leyh, T.S. / Pai, E.F.
History
DepositionMay 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: ATP SULPHURYLASE
B: ATP SULPHURYLASE
C: ATP SULPHURYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,5779
Polymers174,2243
Non-polymers3546
Water9,818545
1
A: ATP SULPHURYLASE
B: ATP SULPHURYLASE
hetero molecules

A: ATP SULPHURYLASE
B: ATP SULPHURYLASE
hetero molecules

A: ATP SULPHURYLASE
B: ATP SULPHURYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)349,08615
Polymers348,4476
Non-polymers6399
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
2
C: ATP SULPHURYLASE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)349,29324
Polymers348,4476
Non-polymers84618
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Unit cell
Length a, b, c (Å)230.850, 230.850, 69.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein ATP SULPHURYLASE / SULFATE ADENYLATE TRANSFERASE / SAT / ATP-SULFURYLASE


Mass: 58074.516 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pSULF2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (Gold) DE3 / References: UniProt: P08536, sulfate adenylyltransferase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 545 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 4% PEG 6000, 1.8 M LiCl, 50 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails (eV)
14 %PEG60001reservoir
21.8 M1reservoirLiCl
350 mMHEPES1reservoirpH7.0
420 %glycerol1reservoir
530-40 mg/mlprotein1drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 14-BM-C11
SYNCHROTRONAPS 14-BM-D2
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJul 2, 2000
ADSC QUANTUM 12CCDFeb 24, 2000
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 353865 / Num. obs: 91000 / % possible obs: 96.4 % / Observed criterion σ(F): 2189 / Observed criterion σ(I): 166 / Redundancy: 4 % / Biso Wilson estimate: 21.4 Å2 / Rsym value: 0.73 / Net I/σ(I): 13.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2 % / Num. unique all: 8242 / Rsym value: 0.461 / % possible all: 87.8
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 30 Å / Num. obs: 73134 / % possible obs: 98.7 % / Num. measured all: 224134 / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
% possible obs: 99.2 % / Rmerge(I) obs: 0.196

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS0.9refinement
RefinementMethod to determine structure: MAD / Resolution: 2.3→29.84 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 296848.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.267 5205 6 %RANDOM
Rwork0.21 ---
obs0.21 86687 91.8 %-
all-353865 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.18 Å2 / ksol: 0.331 e/Å3
Displacement parametersBiso mean: 42.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.78 Å24.22 Å20 Å2
2--2.78 Å20 Å2
3----5.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12269 0 18 545 12832
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.711.5
X-RAY DIFFRACTIONc_mcangle_it7.52
X-RAY DIFFRACTIONc_scbond_it7.142
X-RAY DIFFRACTIONc_scangle_it10.712.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.339 1188 10 %
Rwork0.32 10739 -
obs--76.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION5CIS_PEPTIDE.PARAMCIS_PEPTIDE.TOP
Refinement
*PLUS
Highest resolution: 2.5 Å / Rfactor Rfree: 0.265 / Rfactor Rwork: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg15.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8

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