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- PDB-2qjf: Crystal structure of ATP-sulfurylase domain of human PAPS synthetase 1 -

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Basic information

Entry
Database: PDB / ID: 2qjf
TitleCrystal structure of ATP-sulfurylase domain of human PAPS synthetase 1
ComponentsBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 1
KeywordsTRANSFERASE / ATP-sulfurylase / PAPS-synthetase / monomer-dimer equillibrium
Function / homology
Function and homology information


3'-phosphoadenosine 5'-phosphosulfate biosynthetic process / Transport and synthesis of PAPS / adenylyl-sulfate kinase / sulfate adenylyltransferase / adenylylsulfate kinase activity / sulfate adenylyltransferase (ATP) activity / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / sulfate assimilation / nucleotidyltransferase activity / skeletal system development ...3'-phosphoadenosine 5'-phosphosulfate biosynthetic process / Transport and synthesis of PAPS / adenylyl-sulfate kinase / sulfate adenylyltransferase / adenylylsulfate kinase activity / sulfate adenylyltransferase (ATP) activity / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / sulfate assimilation / nucleotidyltransferase activity / skeletal system development / Signaling by BRAF and RAF1 fusions / phosphorylation / protein homodimerization activity / ATP binding / cytosol
Similarity search - Function
Sulfate adenylyltransferase / Sulfate adenylyltransferase / Sulphate adenylyltransferase / Sulphate adenylyltransferase catalytic domain / ATP-sulfurylase PUA-like domain / ATP-sulfurylase / PUA-like domain / Adenylylsulphate kinase / Adenylyl-sulfate kinase / PUA-like superfamily ...Sulfate adenylyltransferase / Sulfate adenylyltransferase / Sulphate adenylyltransferase / Sulphate adenylyltransferase catalytic domain / ATP-sulfurylase PUA-like domain / ATP-sulfurylase / PUA-like domain / Adenylylsulphate kinase / Adenylyl-sulfate kinase / PUA-like superfamily / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Roll / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-PHOSPHOSULFATE / : / Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSekulic, N. / Lavie, A.
CitationJournal: To be Published
Title: ATP-sulfurylase domain of human bifunctional PAPS-synthetase oscillates between dimeric and monomeric forms
Authors: Sekulic, N. / Paarmann, I. / Konrad, M. / Lavie, A.
History
DepositionJul 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 / 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

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Assembly

Deposited unit
A: Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 1
B: Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,3466
Polymers93,4132
Non-polymers9334
Water12,358686
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-18 kcal/mol
Surface area32820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.100, 99.900, 75.900
Angle α, β, γ (deg.)90.00, 113.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 1 / PAPS synthetase 1 / PAPSS 1 / Sulfurylase kinase 1 / SK1 / SK 1


Mass: 46706.668 Da / Num. of mol.: 2
Fragment: Sulfate adenylyltransferase domain, residue 220-624
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAPSS1, ATPSK1, PAPSS / Plasmid: pGEX-RB / Production host: Escherichia coli (E. coli) / References: UniProt: O43252, sulfate adenylyltransferase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-ADX / ADENOSINE-5'-PHOSPHOSULFATE


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


Mass: 18.015 Da / Num. of mol.: 686 / 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: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: mother liquor: 10% PEG 10K, 0.1M HEPES pH 7.0; protein solution: 10mg/ml, ATP-sulfurylase, 5mM APS, 25mM TRIS/HCl pH 7.5, 25mM KCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.91636501 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 7, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91636501 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 44110 / Num. obs: 43915 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 40.27 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.068 / Net I/σ(I): 12.66
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3.78 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 3.31 / Num. unique all: 5482 / Rsym value: 0.41 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1i2d

1i2d


Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.842 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.299 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22451 4395 10 %RANDOM
Rwork0.16756 ---
all0.17332 44110 --
obs0.17332 39520 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.968 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å2-1.11 Å2
2--0.01 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6277 0 56 686 7019
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226507
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.9658842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8585779
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9423.463309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.279151090
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7121548
X-RAY DIFFRACTIONr_chiral_restr0.0820.2935
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025014
X-RAY DIFFRACTIONr_nbd_refined0.2030.22966
X-RAY DIFFRACTIONr_nbtor_refined0.3050.24372
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2636
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.233
X-RAY DIFFRACTIONr_mcbond_it0.6861.53902
X-RAY DIFFRACTIONr_mcangle_it1.33326282
X-RAY DIFFRACTIONr_scbond_it1.92232623
X-RAY DIFFRACTIONr_scangle_it3.1764.52560
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 350 -
Rwork0.207 2863 -
obs-2863 99.97 %

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