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- PDB-1jed: Crystal Structure of ATP Sulfurylase in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 1jed
TitleCrystal Structure of ATP Sulfurylase in complex with ADP
ComponentsSULFATE ADENYLYLTRANSFERASE
KeywordsTRANSFERASE / alpha-beta protein / beta-barrel / Rossmann-fold / inhibitor complex / ADP
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'-DIPHOSPHATE / : / Sulfate adenylyltransferase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.95 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.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.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.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_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)119,17254
Polymers115,3222
Non-polymers3,85052
Water10,160564
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)357,515162
Polymers345,9666
Non-polymers11,549156
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 area38690 Å2
ΔGint-703 kcal/mol
Surface area116420 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)186.135, 186.135, 223.253
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 , 8 types, 616 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.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: 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
#8: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H4O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 564 / 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 17, 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: 2.95→25 Å / Num. all: 31506 / Num. obs: 31442 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 57.7 Å2 / Rmerge(I) obs: 0.167 / Rsym value: 0.167 / Net I/σ(I): 4.2
Reflection shellResolution: 2.95→3.13 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 1.7 / Num. unique all: 4897 / Rsym value: 0.441 / % possible all: 99.9
Reflection
*PLUS
Rmerge(I) obs: 0.152
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.402

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Processing

Software
NameVersionClassification
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G8G

1g8g


Resolution: 2.95→24.81 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 4314718.28 / 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
Rfree0.227 1616 5.1 %RANDOM
Rwork0.192 ---
all0.192 31506 --
obs0.192 31381 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.25 Å2 / ksol: 0.422 e/Å3
Displacement parametersBiso mean: 30.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å25.08 Å20 Å2
2---0.56 Å20 Å2
3---1.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.95→24.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8150 0 163 564 8877
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it11.5
X-RAY DIFFRACTIONc_mcangle_it1.692
X-RAY DIFFRACTIONc_scbond_it1.62
X-RAY DIFFRACTIONc_scangle_it2.512.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.95→3.13 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.269 278 5.4 %
Rwork0.218 4897 -
obs-4897 100 %
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: 30.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0095
X-RAY DIFFRACTIONc_angle_deg1.54
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.95
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: 0.269 / % reflection Rfree: 5.4 % / Rfactor Rwork: 0.218

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