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- PDB-3db1: Crystal structure of the 2H-phosphatase domain of Sts-2 in comple... -

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Basic information

Entry
Database: PDB / ID: 3db1
TitleCrystal structure of the 2H-phosphatase domain of Sts-2 in complex with phosphate
ComponentsSTS-2 protein
KeywordsHYDROLASE / Sts-2 / 2H-phosphatase / PGM domain / phosphate / SH3 domain
Function / homology
Function and homology information


negative regulation of T cell receptor signaling pathway / regulation of cytokine production / nuclear speck / cytoplasm / cytosol
Similarity search - Function
UBASH3A, SH3 domain / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / UBA/TS-N domain / Variant SH3 domain / Histidine phosphatase superfamily / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily ...UBASH3A, SH3 domain / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / UBA/TS-N domain / 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
PHOSPHATE ION / Ubiquitin-associated and SH3 domain-containing protein A / SH3 domain-containing protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.77 Å
AuthorsNassar, N. / Chen, Y. / Carpino, 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 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / 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 / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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: STS-2 protein
B: STS-2 protein
C: STS-2 protein
D: STS-2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,1507
Polymers122,8654
Non-polymers2853
Water1086
1
A: STS-2 protein
C: STS-2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6234
Polymers61,4332
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-37.2 kcal/mol
Surface area22990 Å2
MethodPISA
2
B: STS-2 protein
D: STS-2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5283
Polymers61,4332
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-26.1 kcal/mol
Surface area22930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.081, 117.025, 121.666
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGCYSCYSAA358 - 3829 - 33
21ARGARGCYSCYSBB358 - 3829 - 33
31ARGARGCYSCYSCC358 - 3829 - 33
41ARGARGCYSCYSDD358 - 3829 - 33
12LYSLYSSERSERAA388 - 40439 - 55
22LYSLYSSERSERBB388 - 40439 - 55
32LYSLYSSERSERCC388 - 40439 - 55
42LYSLYSSERSERDD388 - 40439 - 55
13LYSLYSLYSLYSAA408 - 47959 - 130
23LYSLYSLYSLYSBB408 - 47959 - 130
33LYSLYSLYSLYSCC408 - 47959 - 130
43LYSLYSLYSLYSDD408 - 47959 - 130
14LEULEUASNASNAA490 - 591141 - 242
24LEULEUASNASNBB490 - 591141 - 242
34LEULEUASNASNCC490 - 591141 - 242
44LEULEUASNASNDD490 - 591141 - 242
15LYSLYSASNASNAA596 - 616247 - 267
25LYSLYSASNASNBB596 - 616247 - 267
35LYSLYSASNASNCC596 - 616247 - 267
45LYSLYSASNASNDD596 - 616247 - 267

NCS ensembles :
ID
1
2

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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
Details: T-cells / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ubash3a / Plasmid: pProEX-HTb / Production host: Escherichia coli (E. coli) / Strain (production host): CodonPlus Bl21 / References: UniProt: Q8BX41, UniProt: Q3V3E1*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.3 Å3/Da / Density % sol: 46.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG8000 (w/v), 0.2 M lithium sulfate, 5 to 20 mM strontium chloride, 0.1 M Tris-HCl. Soaked in 0.2 M Na/K phosphate, pH 7.5, 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: Aug 19, 2006 / Details: monochromator
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.77→43.7 Å / Num. all: 28541 / Num. obs: 28141 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Rsym value: 0.101 / Net I/σ(I): 21
Reflection shellResolution: 2.77→2.9 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2.68 / Rsym value: 0.617 / % possible all: 100

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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: 3D4I

3d4i


Resolution: 2.77→43.69 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.904 / SU B: 37.185 / SU ML: 0.339 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.434 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26998 1429 5.1 %RANDOM
Rwork0.24581 ---
obs0.24704 26559 96.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.583 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å20 Å2
2--2.62 Å20 Å2
3----1.62 Å2
Refinement stepCycle: LAST / Resolution: 2.77→43.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8401 0 14 6 8421
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0228608
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3791.97111667
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.17751055
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.21823.265392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.575151502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0451580
X-RAY DIFFRACTIONr_chiral_restr0.0870.21274
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026544
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.230.24040
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.26009
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2283
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3620.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1661.55422
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.04228573
X-RAY DIFFRACTIONr_scbond_it1.71733604
X-RAY DIFFRACTIONr_scangle_it2.724.53094
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1877 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ATIGHT POSITIONAL0.060.05
2BTIGHT POSITIONAL0.050.05
3CTIGHT POSITIONAL0.050.05
4DTIGHT POSITIONAL0.050.05
1ATIGHT THERMAL0.110.5
2BTIGHT THERMAL0.10.5
3CTIGHT THERMAL0.10.5
4DTIGHT THERMAL0.10.5
LS refinement shellResolution: 2.77→2.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 99 -
Rwork0.293 1588 -
obs--81.5 %
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)
10.31880.11490.48891.68620.45382.44270.0227-0.02720.02330.15-0.03890.0864-0.1699-0.28710.0162-0.18370.01040.0386-0.04980.0012-0.1306-39.2066123.21017.3463
23.27640.8139-1.26831.2547-0.26763.04880.1097-0.1170.11540.1528-0.14810.0030.00640.36640.0384-0.09790.04440.01470.07930.014-0.07750.8506109.57947.4445
31.95361.03480.29392.97610.61823.74160.12970.0331-0.06750.53140.0853-0.4649-0.22680.5618-0.2150.0662-0.0024-0.0188-0.06650.0058-0.0107-14.874138.486425.7347
41.65030.0586-0.98111.3647-0.52252.7724-0.0511-0.0406-0.24310.1455-0.0318-0.00460.35310.17760.08290.0589-0.04840.0958-0.13550.0326-0.0761-26.028896.966625.1582
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A357 - 622
2X-RAY DIFFRACTION2B358 - 620
3X-RAY DIFFRACTION3C358 - 621
4X-RAY DIFFRACTION4D358 - 621

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