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- PDB-1jee: Crystal Structure of ATP Sulfurylase in complex with chlorate -

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Basic information

Entry
Database: PDB / ID: 1jee
TitleCrystal Structure of ATP Sulfurylase in complex with chlorate
ComponentsSULFATE ADENYLYLTRANSFERASE
KeywordsTRANSFERASE / alpha-beta protein / beta-barrel / Rossmann-fold / inhibitor complex / chlorate
Function / homology
Function and homology information


sulfate assimilation, phosphoadenylyl sulfate reduction by phosphoadenylyl-sulfate reductase (thioredoxin) / 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 PUA-like domain / ATP-sulfurylase / PUA-like domain / PUA-like superfamily ...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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / ADENOSINE-5'-PHOSPHOSULFATE / : / CHLORATE ION / PYROPHOSPHATE 2- / Sulfate adenylyltransferase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsUllrich, T.C. / Huber, R.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: The complex structures of ATP sulfurylase with thiosulfate, ADP and chlorate reveal new insights in inhibitory effects and the catalytic cycle.
Authors: Ullrich, T.C. / Huber, R.
History
DepositionJun 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _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_asym_id / _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_asym_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_asym_id / _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_asym_id / _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_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
B: SULFATE ADENYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,64256
Polymers115,3222
Non-polymers4,32054
Water10,881604
1
A: SULFATE ADENYLYLTRANSFERASE
B: SULFATE ADENYLYLTRANSFERASE
hetero molecules

A: SULFATE ADENYLYLTRANSFERASE
B: SULFATE ADENYLYLTRANSFERASE
hetero molecules

A: SULFATE ADENYLYLTRANSFERASE
B: SULFATE ADENYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)358,926168
Polymers345,9666
Non-polymers12,960162
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area41330 Å2
ΔGint-670 kcal/mol
Surface area115060 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)185.940, 185.940, 223.812
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
DetailsHomohexamer, generated by the D3 symmetry of the R32 spacegroup (2 different subunits per asymmetric unit)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein SULFATE ADENYLYLTRANSFERASE


Mass: 57661.043 Da / Num. of mol.: 2 / 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 , 10 types, 658 molecules

#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cd
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-LCO / CHLORATE ION


Mass: 83.451 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: ClO3
#7: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2
#8: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#9: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H4O2
#10: Chemical ChemComp-ADX / ADENOSINE-5'-PHOSPHOSULFATE


Type: RNA linking / Mass: 427.284 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O10PS
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 604 / 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: 64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 500 mM NaAc, 50 mM HEPES, 25 mM CdSO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / Details: Ullrich, T.C., (2001) EMBO J., 20, 316.
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: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.542 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 27, 2001 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.8→25 Å / Num. all: 35805 / Num. obs: 35268 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 49.8 Å2 / Rmerge(I) obs: 0.111 / Rsym value: 0.111 / Net I/σ(I): 6.2
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.8 / Num. unique all: 5587 / Rsym value: 0.42 / % possible all: 97.3
Reflection shell
*PLUS
% possible obs: 97.3 % / Rmerge(I) obs: 0.42

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Processing

Software
NameVersionClassification
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G8H

1g8h


Resolution: 2.8→24.87 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3968976.28 / 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
Rfree0.232 1800 5.1 %RANDOM
Rwork0.184 ---
all0.184 35286 --
obs0.184 34984 95.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.56 Å2 / ksol: 0.371 e/Å3
Displacement parametersBiso mean: 34.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å26.94 Å20 Å2
2---0.89 Å20 Å2
3---1.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.8→24.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8150 0 187 604 8941
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_d23.3
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_mcbond_it1.111.5
X-RAY DIFFRACTIONc_mcangle_it1.892
X-RAY DIFFRACTIONc_scbond_it1.662
X-RAY DIFFRACTIONc_scangle_it2.612.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.301 314 5.3 %
Rwork0.246 5587 -
obs-5587 97.3 %
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: 34.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0103
X-RAY DIFFRACTIONc_angle_deg1.52
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.3
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: 0.301 / % reflection Rfree: 5.3 % / Rfactor Rwork: 0.246

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