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- PDB-2ikq: Crystal structure of mouse Sts-1 PGM domain in complex with phosphate -

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Basic information

Entry
Database: PDB / ID: 2ikq
TitleCrystal structure of mouse Sts-1 PGM domain in complex with phosphate
ComponentsSuppressor of T-cell receptor signaling 1
KeywordsSIGNALING PROTEIN / IMMUNE SYSTEM / PGM / acid phosphatase / phospho-histidine enzyme
Function / homology
Function and homology information


regulation of osteoclast differentiation / collagen-activated tyrosine kinase receptor signaling pathway / collagen-activated signaling pathway / negative regulation of platelet aggregation / regulation of release of sequestered calcium ion into cytosol / negative regulation of bone resorption / negative regulation of osteoclast differentiation / negative regulation of signal transduction / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity ...regulation of osteoclast differentiation / collagen-activated tyrosine kinase receptor signaling pathway / collagen-activated signaling pathway / negative regulation of platelet aggregation / regulation of release of sequestered calcium ion into cytosol / negative regulation of bone resorption / negative regulation of osteoclast differentiation / negative regulation of signal transduction / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / phosphoprotein binding / platelet activation / platelet aggregation / ubiquitin protein ligase binding / signal transduction / identical protein binding / nucleus / cytoplasm
Similarity search - Function
UBASH3B, SH3 domain / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / UBA/TS-N domain / Variant SH3 domain / Ubiquitin associated domain / Histidine phosphatase superfamily / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. ...UBASH3B, SH3 domain / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / UBA/TS-N domain / Variant SH3 domain / Ubiquitin associated 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 B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.609 Å
AuthorsChen, Y. / Nassar, N.
CitationJournal: Mol.Cell / Year: 2007
Title: A Phosphatase Activity of Sts-1 Contributes to the Suppression of TCR Signaling
Authors: Mikhailik, A. / Ford, B. / Keller, J. / Chen, Y. / Nassar, N. / Carpino, N.
History
DepositionOct 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / 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_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

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Assembly

Deposited unit
A: Suppressor of T-cell receptor signaling 1
B: Suppressor of T-cell receptor signaling 1
M: Suppressor of T-cell receptor signaling 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3766
Polymers91,0913
Non-polymers2853
Water18010
1
A: Suppressor of T-cell receptor signaling 1
B: Suppressor of T-cell receptor signaling 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9174
Polymers60,7282
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-43 kcal/mol
Surface area23060 Å2
MethodPISA, PQS
2
M: Suppressor of T-cell receptor signaling 1
hetero molecules

M: Suppressor of T-cell receptor signaling 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9174
Polymers60,7282
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
MethodPQS
Unit cell
Length a, b, c (Å)116.960, 74.671, 101.279
Angle α, β, γ (deg.)90.00, 100.79, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31M
41A
51B
61M
71A
81B
91M
12A
22M
13A
23B

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ARGARGGLUGLU1AA373 - 4905 - 122
211ARGARGGLUGLU1BB373 - 4905 - 122
311ARGARGGLUGLU1MC373 - 4905 - 122
421THRTHRGLUGLU1AA499 - 603131 - 235
521THRTHRGLUGLU1BB499 - 603131 - 235
621THRTHRGLUGLU1MC499 - 603131 - 235
731TRPTRPTHRTHR1AA611 - 626243 - 258
831TRPTRPTHRTHR1BB611 - 626243 - 258
931TRPTRPTHRTHR1MC611 - 626243 - 258
112GLUGLUILEILE1AA604 - 610236 - 242
212GLUGLUILEILE1MC604 - 610236 - 242
113GLUGLUILEILE6AA604 - 610236 - 242
213GLUGLUILEILE6BB604 - 610236 - 242

NCS ensembles :
ID
1
2
3
DetailsSubunits A and B form a dimer. Subunit C dimerizes with its symmetry generated by the 2-fold axis: -x, y, -z

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Components

#1: Protein Suppressor of T-cell receptor signaling 1 / Sts-1 / Cbl-interacting protein p70


Mass: 30363.771 Da / Num. of mol.: 3
Fragment: phosphoglycerate mutase homology domain, residues 373-633
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sts-1 / Plasmid: pProEX-2Hb / Production host: Escherichia coli (E. coli) / Strain (production host): CodonPlus / References: UniProt: Q8BGG7
#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.: 10 / 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: 2.38 Å3/Da / Density % sol: 48.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 14% PEG 8000, 0.1 M HEPES, 0.3 M Na Acetate, 0.2 M Na/K phosphate, pH 7.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 15, 2006
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.609→100 Å / Num. all: 25668 / Num. obs: 25668 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 74.8 Å2 / Rmerge(I) obs: 0.63 / Rsym value: 0.63 / Net I/σ(I): 30
Reflection shellResolution: 2.609→2.69 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 3.2 / Num. unique all: 2582 / Rsym value: 0.556 / % possible all: 99.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
CCP4model building
REFMAC5.2refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1H0Q

1h0q


Resolution: 2.609→99.5 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.908 / SU B: 36.002 / SU ML: 0.335 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.369 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27515 1293 5 %RANDOM
Rwork0.24773 ---
obs0.2491 24371 97.58 %-
all-25664 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.359 Å2
Baniso -1Baniso -2Baniso -3
1--4.21 Å20 Å2-1.42 Å2
2--8.82 Å20 Å2
3----5.15 Å2
Refine analyzeLuzzati coordinate error free: 0.372 Å / Luzzati sigma a free: 0.333 Å
Refinement stepCycle: LAST / Resolution: 2.609→99.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6103 0 15 10 6128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226269
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.421.9568518
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3595773
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.68123.663273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.431151051
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9431540
X-RAY DIFFRACTIONr_chiral_restr0.0950.2939
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024743
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2440.22739
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.24281
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2220
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3670.2130
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.430.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7071.53962
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.29426282
X-RAY DIFFRACTIONr_scbond_it1.49432626
X-RAY DIFFRACTIONr_scangle_it2.3124.52236
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A3627tight positional0.060.05
12B3627tight positional0.070.05
13M3627tight positional0.050.05
21A87tight positional0.020.05
31A87loose positional0.375
11A3627tight thermal0.120.5
12B3627tight thermal0.090.5
13M3627tight thermal0.070.5
21A87tight thermal0.060.5
31A87loose thermal3.6210
LS refinement shellResolution: 2.609→2.677 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.381 90
Rwork0.371 1768

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