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- PDB-3d6a: Crystal structure of the 2H-phosphatase domain of Sts-2 in comple... -

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Basic information

Entry
Database: PDB / ID: 3d6a
TitleCrystal structure of the 2H-phosphatase domain of Sts-2 in complex with tungstate.
ComponentsSts-2 protein
KeywordsHYDROLASE / 2H-phosphatase / PGM domain / tungstate / SH3 domain
Function / homology
Function and homology information


negative regulation of T cell receptor signaling pathway / regulation of cytokine production / nuclear speck / cytosol
Similarity search - Function
UBASH3A, SH3 domain / : / UBA-like domain / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Variant SH3 domain / Histidine phosphatase superfamily / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. ...UBASH3A, SH3 domain / : / UBA-like domain / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Variant SH3 domain / Histidine phosphatase superfamily / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Ubiquitin-associated and SH3 domain-containing protein A / Ubiquitin-associated and SH3 domain-containing protein A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.25 Å
AuthorsChen, Y. / Carpino, N. / Nassar, N.
CitationJournal: Biochemistry / Year: 2009
Title: Structural and functional characterization of the 2H-phosphatase domain of Sts-2 reveals an acid-dependent phosphatase activity.
Authors: Chen, Y. / Jakoncic, J. / Carpino, N. / Nassar, N.
History
DepositionMay 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 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 / pdbx_struct_conn_angle / 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_asym_id / _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
Revision 1.3Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sts-2 protein
B: Sts-2 protein
C: Sts-2 protein
D: Sts-2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,91121
Polymers122,8654
Non-polymers1,04617
Water3,135174
1
A: Sts-2 protein
C: Sts-2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,99212
Polymers61,4332
Non-polymers55910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
ΔGint-100.1 kcal/mol
Surface area23410 Å2
MethodPISA
2
B: Sts-2 protein
D: Sts-2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9199
Polymers61,4332
Non-polymers4877
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-80.1 kcal/mol
Surface area23400 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15580 Å2
ΔGint-195.9 kcal/mol
Surface area43070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.205, 116.665, 121.471
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Sts-2 protein


Mass: 30716.334 Da / Num. of mol.: 4 / Fragment: PGM domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ubash3a / Plasmid: pProEx-HTb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8BX41, UniProt: Q3V3E1*PLUS
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-W / TUNGSTEN ION


Mass: 183.840 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: W
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.26 Å3/Da / Density % sol: 45.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M Lithium sulfate, 0.1 M Tris-HCl, 5-20 mM Strontium chloride, 20% PEG8000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 20, 2006 / Details: monochromator
RadiationMonochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→100 Å / Num. all: 53723 / Num. obs: 53273 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Rmerge(I) obs: 0.098
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.5 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3d4i

3d4i


Resolution: 2.25→47.95 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.919 / SU B: 11.188 / SU ML: 0.167 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.348 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25672 2704 5.1 %RANDOM
Rwork0.20824 ---
obs0.21068 50569 99.17 %-
all-50569 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.185 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å20 Å2
2--0.8 Å20 Å2
3----1.34 Å2
Refinement stepCycle: LAST / Resolution: 2.25→47.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8414 0 17 174 8605
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0228622
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2441.9711684
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.97751057
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.07823.265392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.249151505
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4541580
X-RAY DIFFRACTIONr_chiral_restr0.090.21281
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026536
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.23794
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.25804
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2343
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.4680.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7041.55305
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.31828584
X-RAY DIFFRACTIONr_scbond_it1.56633457
X-RAY DIFFRACTIONr_scangle_it2.5364.53100
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.304 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 209 -
Rwork0.235 3550 -
obs--95.82 %
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)
10.2773-0.00490.35810.6611-0.15631.17140.0094-0.0275-0.02640.02410.0080.0961-0.0729-0.1735-0.0173-0.05170.0170.01930.011-0.0033-0.0292-39.3148122.6127.438
21.18370.2386-0.48840.5785-0.42651.44880.02280.04250.02970.0691-0.1011-0.01610.05940.25210.0783-0.07850.02110.01820.06730.0259-0.07031.0806109.4087.7406
30.66150.39360.2870.93630.05841.35860.05380.0657-0.06640.1707-0.0565-0.1469-0.25330.08320.00270.045-0.0219-0.0073-0.07590.0253-0.0329-14.5701137.889425.3678
40.6967-0.0499-0.18630.667-0.52711.2340.01650.0048-0.09750.00920.02620.08160.17980.0643-0.04270.0249-0.0230.0391-0.06280.0125-0.0417-25.957196.532525.1107
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA357 - 6228 - 273
2X-RAY DIFFRACTION2BB358 - 6219 - 272
3X-RAY DIFFRACTION3CC358 - 6229 - 273
4X-RAY DIFFRACTION4DD357 - 6228 - 273

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