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- PDB-2ax4: Crystal structure of the kinase domain of human 3'-phosphoadenosi... -

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Basic information

Entry
Database: PDB / ID: 2ax4
TitleCrystal structure of the kinase domain of human 3'-phosphoadenosine 5'-phosphosulphate synthetase 2
ComponentsBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 2
KeywordsTRANSFERASE / PAPSS2 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Defective PAPSS2 causes SEMD-PA / 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 / hormone metabolic process ...Defective PAPSS2 causes SEMD-PA / 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 / hormone metabolic process / nucleotidyltransferase activity / bone development / blood coagulation / phosphorylation / ATP binding / cytosol
Similarity search - Function
Sulphate adenylyltransferase / Sulphate adenylyltransferase catalytic domain / ATP-sulfurylase PUA-like domain / ATP-sulfurylase / PUA-like domain / Adenylylsulphate kinase / Adenylyl-sulfate 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 / Adenylylsulphate kinase / Adenylyl-sulfate kinase / PUA-like superfamily / Rossmann-like alpha/beta/alpha sandwich fold / P-loop containing nucleotide triphosphate hydrolases / 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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRabeh, W.M. / Nedyalkova, L. / Ismail, S. / Park, H. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the kinase domain of PAPSS 2
Authors: Rabeh, W.M. / Nedyalkova, L. / Ismail, S. / Park, H. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / Weigelt, J. / Bochkarev, A.
History
DepositionSep 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_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: Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 2
B: Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 2
C: Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 2
D: Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4608
Polymers87,7514
Non-polymers1,7094
Water5,260292
1
A: Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 2
B: Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7304
Polymers43,8762
Non-polymers8542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-30 kcal/mol
Surface area17000 Å2
MethodPISA
2
C: Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 2
D: Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7304
Polymers43,8762
Non-polymers8542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-31 kcal/mol
Surface area16980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.914, 131.892, 70.562
Angle α, β, γ (deg.)90.00, 104.58, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 1 / Auth seq-ID: 34 - 228 / Label seq-ID: 4 - 198

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 2 / Adenylylsulfate 3'-phosphotransferase / Adenosine-5'-phosphosulfate 3'-phosphotransferase / 3'- ...Adenylylsulfate 3'-phosphotransferase / Adenosine-5'-phosphosulfate 3'-phosphotransferase / 3'-phosphoadenosine-5'-phosphosulfate synthetase


Mass: 21937.809 Da / Num. of mol.: 4 / Fragment: APS Kinase domain (residues 21-218)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAPSS2 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O95340, adenylyl-sulfate kinase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


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


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.7 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: PEG3350 18%, 0.2M Ammonium Citrate, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 20, 2005
RadiationMonochromator: CONFOCAL MAXFLUX OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 31749 / % possible obs: 98.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rsym value: 0.12 / Net I/σ(I): 13.14
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 4.88 / Rsym value: 0.344 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.836 / SU B: 10.329 / SU ML: 0.232 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.698 / ESU R Free: 0.332 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27835 1601 5.1 %RANDOM
Rwork0.21159 ---
obs0.215 30052 97.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.764 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20.22 Å2
2---0.92 Å20 Å2
3---1.27 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6128 0 108 292 6528
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226362
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6681.9798620
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0865782
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4123.133300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.446151058
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5221560
X-RAY DIFFRACTIONr_chiral_restr0.1080.2946
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024844
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2230.22908
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.24330
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2404
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.269
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7061.53965
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.21926262
X-RAY DIFFRACTIONr_scbond_it1.99832655
X-RAY DIFFRACTIONr_scangle_it3.2074.52358
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.501→2.566 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 124 -
Rwork0.248 2176 -
obs--97.5 %

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