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- PDB-1g8f: ATP SULFURYLASE FROM S. CEREVISIAE -

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Basic information

Entry
Database: PDB / ID: 1g8f
TitleATP SULFURYLASE FROM S. CEREVISIAE
ComponentsSULFATE ADENYLYLTRANSFERASE
KeywordsTRANSFERASE / alpha-beta protein / beta-barrel / Rossmann-fold / kinase fold
Function / homology
Function and homology information


sulfur amino acid metabolic process / sulfate assimilation via adenylyl sulfate reduction / sulfate assimilation, phosphoadenylyl sulfate reduction by phosphoadenylyl-sulfate reductase (thioredoxin) / 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 PUA-like domain / ATP-sulfurylase / PUA-like domain / PUA-like superfamily / HUPs ...Sulfate adenylyltransferase / Sulfate adenylyltransferase / Sulfate adenylyltransferase / Sulphate adenylyltransferase / Sulphate adenylyltransferase catalytic domain / ATP-sulfurylase PUA-like domain / ATP-sulfurylase / PUA-like domain / PUA-like superfamily / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / P-loop containing nucleotide triphosphate hydrolases / Roll / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / : / Sulfate adenylyltransferase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.95 Å
AuthorsUllrich, T.C. / Blaesse, M. / Huber, R.
CitationJournal: EMBO J. / Year: 2001
Title: Crystal structure of ATP sulfurylase from Saccharomyces cerevisiae, a key enzyme in sulfate activation.
Authors: Ullrich, T.C. / Blaesse, M. / Huber, R.
History
DepositionNov 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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

Downloads & links

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Assembly

Deposited unit
A: SULFATE ADENYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,54926
Polymers57,8211
Non-polymers1,72725
Water10,196566
1
A: SULFATE ADENYLYLTRANSFERASE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)357,292156
Polymers346,9276
Non-polymers10,364150
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
Buried area33280 Å2
ΔGint-680 kcal/mol
Surface area120950 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)187.094, 187.094, 115.999
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-515-

CD

21A-520-

CA

DetailsThe biological assembly is a homo-hexamer generated from the monomer in the asymmtric unit by the triad and the perpendicular dyad axis (D3 symmetry)of the R32 spacegroup

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Components

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Protein , 1 types, 1 molecules A

#1: Protein SULFATE ADENYLYLTRANSFERASE / / ATP-SULFURYLASE / SAT


Mass: 57821.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NATIVE PURIFICATION OUT OF YEAST CELLS / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: S288C/FY1679 / References: UniProt: P08536, sulfate adenylyltransferase

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Non-polymers , 8 types, 591 molecules

#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Chemical
ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H4O2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 566 / 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: 3.38 Å3/Da / Density % sol: 63.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 500 mM Sodium acetate, 50 mM HEPES, 25 mM Cadmium sulfate , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
220 mMTris-HCl1drop
31 mMEDTA1drop
41 mM1dropNaN3
50.5 M1reservoirNaOAc
650 mMHEPES1reservoir
725 mM1reservoirCdSO4

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.042 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 12, 2000 / Details: Double focussing x-ray optics
RadiationMonochromator: double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.042 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. all: 55756 / Num. obs: 55315 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 19.8 Å2 / Rsym value: 0.051 / Net I/σ(I): 9.3
Reflection shellResolution: 1.95→2.07 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 8767 / Rsym value: 0.28 / % possible all: 98.6
Reflection
*PLUS
Rmerge(I) obs: 0.051
Reflection shell
*PLUS
% possible obs: 98.6 % / Rmerge(I) obs: 0.28

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Processing

Software
NameVersionClassification
CCP4model building
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 1.95→19.68 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3832033.19 / Data cutoff high rms absF: 3832033.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.231 2835 5.1 %RANDOM
Rwork0.196 ---
all0.196 55315 --
obs0.196 55315 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.13 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 35.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.39 Å2-0.09 Å20 Å2
2---2.39 Å20 Å2
3---4.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.95→19.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4077 0 73 566 4716
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_mcbond_it1.391.5
X-RAY DIFFRACTIONc_mcangle_it2.082
X-RAY DIFFRACTIONc_scbond_it2.152
X-RAY DIFFRACTIONc_scangle_it3.062.5
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.279 449 4.9 %
Rwork0.244 8767 -
obs-8767 98.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4ACY.PARACY.TOP
X-RAY DIFFRACTION5TRS.PARTRS.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 35.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.96
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.279 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.244

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