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- PDB-3ap3: Crystal structure of human tyrosylprotein sulfotransferase-2 comp... -

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Basic information

Entry
Database: PDB / ID: 3ap3
TitleCrystal structure of human tyrosylprotein sulfotransferase-2 complexed with PAP
ComponentsProtein-tyrosine sulfotransferase 2
KeywordsTRANSFERASE / sulfotransferase fold
Function / homology
Function and homology information


peptidyl-tyrosine sulfation / protein-tyrosine sulfotransferase / protein-tyrosine sulfotransferase activity / Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation / Defective F8 sulfation at Y1699 / Cytosolic sulfonation of small molecules / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / Golgi membrane / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity
Similarity search - Function
Protein-tyrosine sulfotransferase / Sulfotransferase family / 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-3'-5'-DIPHOSPHATE / Protein-tyrosine sulfotransferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsTeramoto, T. / Fujikawa, Y. / Kawaguchi, Y. / Kurogi, K. / Soejima, M. / Adachi, R. / Nakanishi, Y. / Mishiro-Sato, E. / Liu, M.-C. / Sakakibara, Y. ...Teramoto, T. / Fujikawa, Y. / Kawaguchi, Y. / Kurogi, K. / Soejima, M. / Adachi, R. / Nakanishi, Y. / Mishiro-Sato, E. / Liu, M.-C. / Sakakibara, Y. / Suiko, M. / Kimura, M. / Kakuta, Y.
CitationJournal: Nat Commun / Year: 2013
Title: Crystal structure of human tyrosylprotein sulfotransferase-2 reveals the mechanism of protein tyrosine sulfation reaction.
Authors: Teramoto, T. / Fujikawa, Y. / Kawaguchi, Y. / Kurogi, K. / Soejima, M. / Adachi, R. / Nakanishi, Y. / Mishiro-Sato, E. / Liu, M.C. / Sakakibara, Y. / Suiko, M. / Kimura, M. / Kakuta, Y.
History
DepositionOct 9, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references
Revision 1.2Nov 1, 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

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Assembly

Deposited unit
A: Protein-tyrosine sulfotransferase 2
B: Protein-tyrosine sulfotransferase 2
C: Protein-tyrosine sulfotransferase 2
D: Protein-tyrosine sulfotransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,2648
Polymers158,5554
Non-polymers1,7094
Water00
1
A: Protein-tyrosine sulfotransferase 2
B: Protein-tyrosine sulfotransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1324
Polymers79,2772
Non-polymers8542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-25 kcal/mol
Surface area24790 Å2
MethodPISA
2
C: Protein-tyrosine sulfotransferase 2
D: Protein-tyrosine sulfotransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1324
Polymers79,2772
Non-polymers8542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-22 kcal/mol
Surface area25020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.432, 81.326, 226.659
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

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Components

#1: Protein
Protein-tyrosine sulfotransferase 2 / Tyrosylprotein sulfotransferase 2 / TPST-2


Mass: 39638.688 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 43-377
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TPST2 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O60704, protein-tyrosine sulfotransferase
#2: Chemical
ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2

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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: 2.08 Å3/Da / Density % sol: 40.75 %
Crystal growTemperature: 283.4 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Tris-HCl, pH 7.0, 0.1M calcium acetate, 20 % polyethylene glycol 3000, VAPOR DIFFUSION, SITTING DROP, temperature 283.4K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. all: 11529 / Num. obs: 11529 / % possible obs: 68.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.164 / Rsym value: 0.165 / Net I/σ(I): 16.5
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 3 / Num. unique all: 364 / Rsym value: 0.464 / % possible all: 42.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AP1

3ap1


Resolution: 3.5→48.5 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.824 / SU B: 57.558 / SU ML: 0.893 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 1.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3709 583 5 %RANDOM
Rwork0.29026 ---
obs0.29398 11066 67.08 %-
all-11066 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 124.515 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å20 Å2
2--0.65 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 3.5→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9002 0 108 0 9110
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0229357
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.99212698
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.62651145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.56222.809388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.255151646
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2591582
X-RAY DIFFRACTIONr_chiral_restr0.0810.21413
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216935
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3311.55723
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.65529260
X-RAY DIFFRACTIONr_scbond_it0.95633634
X-RAY DIFFRACTIONr_scangle_it1.7954.53434
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2125 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.220.5
Bmedium positional0.230.5
Cmedium positional0.210.5
Dmedium positional0.20.5
Amedium thermal0.342
Bmedium thermal0.482
Cmedium thermal0.272
Dmedium thermal0.32
LS refinement shellResolution: 3.5→3.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 31 -
Rwork0.366 483 -
obs--41.12 %

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