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- PDB-2ofw: Crystal structure of the APSK domain of human PAPSS1 complexed wi... -

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Basic information

Entry
Database: PDB / ID: 2ofw
TitleCrystal structure of the APSK domain of human PAPSS1 complexed with 2 APS molecules
ComponentsAPS kinase domain of the PAPS synthetase 1
KeywordsTRANSFERASE / nucleotide kinase
Function / homology
Function and homology information


3'-phosphoadenosine 5'-phosphosulfate biosynthetic process / Transport and metabolism 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 metabolism 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 / protein homodimerization activity / ATP binding / nucleus / cytosol
Similarity search - Function
Sulphate adenylyltransferase / Sulphate adenylyltransferase catalytic domain / ATP-sulfurylase PUA-like domain / ATP-sulfurylase / PUA-like domain / Adenylyl-sulfate kinase / Adenylylsulphate kinase / PUA-like superfamily / Rossmann-like alpha/beta/alpha sandwich fold / P-loop containing nucleotide triphosphate hydrolases ...Sulphate adenylyltransferase / Sulphate adenylyltransferase catalytic domain / ATP-sulfurylase PUA-like domain / ATP-sulfurylase / PUA-like domain / Adenylyl-sulfate kinase / Adenylylsulphate kinase / PUA-like superfamily / Rossmann-like alpha/beta/alpha sandwich fold / P-loop containing nucleotide triphosphate hydrolases / 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: 2.05 Å
AuthorsSekulic, N. / Lavie, A.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Elucidation of the Active Conformation of the APS-Kinase Domain of Human PAPS Synthetase 1.
Authors: Sekulic, N. / Dietrich, K. / Paarmann, I. / Ort, S. / Konrad, M. / Lavie, A.
History
DepositionJan 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Advisory / Structure summary / Category: audit_author / pdbx_unobs_or_zero_occ_atoms / Item: _audit_author.name
Revision 1.4Aug 30, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_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.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_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_conn.ptnr2_label_seq_id / _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: APS kinase domain of the PAPS synthetase 1
B: APS kinase domain of the PAPS synthetase 1
C: APS kinase domain of the PAPS synthetase 1
D: APS kinase domain of the PAPS synthetase 1
E: APS kinase domain of the PAPS synthetase 1
F: APS kinase domain of the PAPS synthetase 1
G: APS kinase domain of the PAPS synthetase 1
H: APS kinase domain of the PAPS synthetase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,78330
Polymers184,8018
Non-polymers6,98222
Water14,988832
1
A: APS kinase domain of the PAPS synthetase 1
B: APS kinase domain of the PAPS synthetase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9347
Polymers46,2002
Non-polymers1,7335
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6810 Å2
ΔGint-62 kcal/mol
Surface area16100 Å2
MethodPISA
2
C: APS kinase domain of the PAPS synthetase 1
D: APS kinase domain of the PAPS synthetase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9588
Polymers46,2002
Non-polymers1,7586
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8700 Å2
ΔGint-80 kcal/mol
Surface area15850 Å2
MethodPISA
3
E: APS kinase domain of the PAPS synthetase 1
F: APS kinase domain of the PAPS synthetase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9588
Polymers46,2002
Non-polymers1,7586
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8470 Å2
ΔGint-76 kcal/mol
Surface area15950 Å2
MethodPISA
4
G: APS kinase domain of the PAPS synthetase 1
H: APS kinase domain of the PAPS synthetase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9347
Polymers46,2002
Non-polymers1,7335
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6830 Å2
ΔGint-64 kcal/mol
Surface area16120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.190, 69.030, 150.610
Angle α, β, γ (deg.)90.000, 116.610, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
APS kinase domain of the PAPS synthetase 1


Mass: 23100.082 Da / Num. of mol.: 8 / Fragment: APS kinse domain (Residues 1-227)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAPSS1, ATPSK1, PAPSS / Plasmid: pGEX-RB with engineered TEV cutting site / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 Codon Plus / References: UniProt: O43252, adenylyl-sulfate kinase
#2: Chemical
ChemComp-ADX / ADENOSINE-5'-PHOSPHOSULFATE


Type: RNA linking / Mass: 427.284 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C10H14N5O10PS
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 832 / 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: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: reservoir: 18-20% PEG 3350, 0.25 M calcium acetate protein solution: 5-8 mg/ml protein, 3 mM APS, 5 mM MgCl2, 50 mM Tris pH 7.5, 50 mM KCl, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.9594 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 17, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9594 Å / Relative weight: 1
ReflectionResolution: 2.05→10 Å / Num. all: 121588 / Num. obs: 101698 / % possible obs: 83.6 % / Observed criterion σ(F): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.095 / Rsym value: 0.082 / Net I/σ(I): 12.4
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 4.36 / Num. unique all: 7260 / Rsym value: 0.24 / % possible all: 92.8

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Phasing

Phasing MRRfactor: 0.532 / Cor.coef. Fo:Fc: 0.272
Highest resolutionLowest resolution
Rotation5 Å19.95 Å
Translation5 Å19.95 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb id 1M7G

1m7g


Resolution: 2.05→10 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.877 / SU B: 6.244 / SU ML: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.285 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.282 10107 10 %RANDOM
Rwork0.217 ---
obs0.223 101066 97.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.759 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å2-0.02 Å2
2---0.65 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.05→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12417 0 438 832 13687
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02213094
X-RAY DIFFRACTIONr_angle_refined_deg1.7292.00117819
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.80751597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.36224.304618
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.318152123
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2091599
X-RAY DIFFRACTIONr_chiral_restr0.0870.21953
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210035
X-RAY DIFFRACTIONr_nbd_refined0.2040.26185
X-RAY DIFFRACTIONr_nbtor_refined0.3020.28660
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2979
X-RAY DIFFRACTIONr_metal_ion_refined0.2010.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1450.291
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.234
X-RAY DIFFRACTIONr_mcbond_it0.6111.58183
X-RAY DIFFRACTIONr_mcangle_it1.021212771
X-RAY DIFFRACTIONr_scbond_it1.57535603
X-RAY DIFFRACTIONr_scangle_it2.4034.55048
LS refinement shellResolution: 2.05→2.101 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 703 -
Rwork0.234 6163 -
obs-6866 92.93 %

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