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- PDB-1x6v: The crystal structure of human 3'-phosphoadenosine-5'-phosphosulf... -

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Basic information

Entry
Database: PDB / ID: 1x6v
TitleThe crystal structure of human 3'-phosphoadenosine-5'-phosphosulfate synthetase 1
ComponentsBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 1
KeywordsTRANSFERASE / ATP sulfurylase / APS kinase / PAPS / phosphoadenosine phosphosulfate
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 / 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
ADENOSINE-5'-DIPHOSPHATE / Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT WITH INITIAL MERCURY PHASES / Resolution: 1.75 Å
AuthorsHarjes, S. / Bayer, P. / Scheidig, A.J.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: The Crystal Structure of Human PAPS Synthetase 1 Reveals Asymmetry in Substrate Binding
Authors: Harjes, S. / Bayer, P. / Scheidig, A.J.
History
DepositionAug 12, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2013Group: Advisory / Other
Revision 1.4Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_validate_close_contact / software
Item: _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 ..._pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _software.name
Revision 1.5Aug 23, 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_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)143,8965
Polymers143,3982
Non-polymers4983
Water19,6541091
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-52 kcal/mol
Surface area48770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.210, 82.550, 133.600
Angle α, β, γ (deg.)90.00, 105.10, 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: 71698.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: [Includes: Sulfate adenylyltransferase (synonym: Sulfate adenylate transferase, SAT, ATP-sulfurylase); Adenylyl-sulfate kinase (synonym: Adenylylsulfate 3'-phosphotransferase, APS kinase, ...Details: [Includes: Sulfate adenylyltransferase (synonym: Sulfate adenylate transferase, SAT, ATP-sulfurylase); Adenylyl-sulfate kinase (synonym: Adenylylsulfate 3'-phosphotransferase, APS kinase, Adenosine-5'-phosphosulfate 3'-phosphotransferase, 3'- phosphoadenosine-5'-phosphosulfate synthetase)]
Source: (gene. exp.) Homo sapiens (human) / Gene: PAPSS1, PAPSS, ATPSK1 / Plasmid: pET27bmod / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: O43252, sulfate adenylyltransferase, adenylyl-sulfate kinase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1091 / 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: 2.9 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 285 K / pH: 5.6
Details: 91 mM sodium Citrate, 270 mM ammonium acetate, 12% PEG 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 159267 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rsym value: 0.069 / Net I/σ(I): 11
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.58 / % possible all: 88

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
X-GENdata reduction
XDSdata scaling
XFITdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT WITH INITIAL MERCURY PHASES
Starting model: PDB ENTRIES 1G8F, 1D6J

1g8f

1d6j


Resolution: 1.75→129.1 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.311 / SU ML: 0.07 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19811 8203 5 %RANDOM
Rwork0.1663 ---
obs0.16789 156571 99.69 %-
all-165305 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.273 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å20.24 Å2
2--1.4 Å20 Å2
3----0.86 Å2
Refinement stepCycle: LAST / Resolution: 1.75→129.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9192 0 29 1091 10312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0219456
X-RAY DIFFRACTIONr_bond_other_d0.0020.028508
X-RAY DIFFRACTIONr_angle_refined_deg1.8051.95412811
X-RAY DIFFRACTIONr_angle_other_deg1.48319822
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.91351145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.130.21376
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0210479
X-RAY DIFFRACTIONr_gen_planes_other0.0140.021925
X-RAY DIFFRACTIONr_nbd_refined0.2290.21908
X-RAY DIFFRACTIONr_nbd_other0.260.29773
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0880.25291
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2270.2806
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2720.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2990.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2271.55727
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.16329243
X-RAY DIFFRACTIONr_scbond_it3.0733729
X-RAY DIFFRACTIONr_scangle_it4.9324.53567
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.324 591
Rwork0.297 11126
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.44790.31750.00170.3927-0.02590.0850.00840.0022-0.01090.00910.0105-0.01450.01590.0119-0.0190.07940.02180.00830.0133-0.01060.023426.131552.344963.4645
20.16640.0672-0.05150.1191-0.03090.0680.00870.0251-0.00590.0041-0.020.00110.00180.00070.01120.0322-0.0073-0.00840.0439-0.00550.036225.835530.090421.241
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AB34 - 22534 - 225
2X-RAY DIFFRACTION1BA34 - 22534 - 225
3X-RAY DIFFRACTION2AB234 - 624234 - 624
4X-RAY DIFFRACTION2BA234 - 623234 - 623

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