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- PDB-3ap1: Crystal structure of human tyrosylprotein sulfotransferase-2 comp... -

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Basic information

Entry
Database: PDB / ID: 3ap1
TitleCrystal structure of human tyrosylprotein sulfotransferase-2 complexed with PAP and C4 peptide
Components
  • C4 peptide
  • Protein-tyrosine sulfotransferase 2
KeywordsTRANSFERASE / sulfotransferase fold
Function / homology
Function and homology information


peptidyl-tyrosine sulfation / protein-tyrosine sulfotransferase / protein-tyrosine sulfotransferase activity / Defective F8 sulfation at Y1699 / Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation / 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 / SIRAS / Resolution: 1.9 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 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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
S: C4 peptide
T: C4 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8507
Polymers77,9044
Non-polymers9463
Water5,747319
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6280 Å2
ΔGint-29 kcal/mol
Surface area24640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.263, 138.263, 227.994
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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


Mass: 37743.656 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 43-359
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: Protein/peptide C4 peptide


Mass: 1208.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemical synthesis
#3: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.69 Å3/Da / Density % sol: 54.3 %
Crystal growTemperature: 293.4 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M sodium malonate (pH 5.0), 10% polyethylene glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293.4K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / 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: 1.9→50 Å / Num. all: 65960 / Num. obs: 65960 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.108 / Rsym value: 0.108 / Net I/σ(I): 12.5
Reflection shellResolution: 1.9→50 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.108 / Mean I/σ(I) obs: 12.5 / Num. unique all: 65960 / Rsym value: 0.108 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.9→33.3 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.115 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22165 3337 5.1 %RANDOM
Rwork0.19522 ---
obs0.19658 62512 99.79 %-
all-62512 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.322 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→33.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4854 0 60 319 5233
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225179
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.997039
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6455644
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.63323.216227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.22815925
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1191544
X-RAY DIFFRACTIONr_chiral_restr0.1040.2775
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213876
X-RAY DIFFRACTIONr_mcbond_it0.6881.53135
X-RAY DIFFRACTIONr_mcangle_it1.26725085
X-RAY DIFFRACTIONr_scbond_it2.05432044
X-RAY DIFFRACTIONr_scangle_it3.3164.51938
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 250 -
Rwork0.314 4532 -
obs--99.15 %

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