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- PDB-2yz1: Crystal structure of the ligand-binding domain of murine SHPS-1/S... -

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Basic information

Entry
Database: PDB / ID: 2yz1
TitleCrystal structure of the ligand-binding domain of murine SHPS-1/SIRP alpha
ComponentsTyrosine-protein phosphatase non-receptor type substrate 1
KeywordsIMMUNE SYSTEM / BETA-SANDWICH / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / Alternative splicing / Glycoprotein / Immunoglobulin domain / Membrane / Phosphorylation / Polymorphism / SH3-binding / Transmembrane
Function / homology
Function and homology information


Signal regulatory protein family interactions / negative regulation of I-kappaB phosphorylation / cellular response to interleukin-12 / monocyte extravasation / negative regulation of macrophage inflammatory protein 1 alpha production / granulocyte migration / negative regulation of chemokine (C-C motif) ligand 5 production / protein binding involved in heterotypic cell-cell adhesion / protein phosphorylated amino acid binding / regulation of interleukin-1 beta production ...Signal regulatory protein family interactions / negative regulation of I-kappaB phosphorylation / cellular response to interleukin-12 / monocyte extravasation / negative regulation of macrophage inflammatory protein 1 alpha production / granulocyte migration / negative regulation of chemokine (C-C motif) ligand 5 production / protein binding involved in heterotypic cell-cell adhesion / protein phosphorylated amino acid binding / regulation of interleukin-1 beta production / regulation of type II interferon production / GTPase regulator activity / Cell surface interactions at the vascular wall / positive regulation of cell-cell adhesion / cell-cell adhesion mediator activity / protein antigen binding / negative regulation of nitric oxide biosynthetic process / phagocytosis, recognition / negative regulation of interferon-beta production / negative regulation of JNK cascade / regulation of tumor necrosis factor production / regulation of nitric oxide biosynthetic process / negative regulation of phagocytosis / DAP12 interactions / regulation of interleukin-6 production / phagocytosis, engulfment / plasma membrane => GO:0005886 / negative regulation of interleukin-6 production / negative regulation of tumor necrosis factor production / negative regulation of cytokine production involved in inflammatory response / cellular response to interleukin-1 / hematopoietic progenitor cell differentiation / positive regulation of phagocytosis / cytoskeleton organization / Neutrophil degranulation / cell-matrix adhesion / protein tyrosine kinase binding / negative regulation of protein phosphorylation / actin filament organization / negative regulation of ERK1 and ERK2 cascade / negative regulation of inflammatory response / SH3 domain binding / cellular response to type II interferon / cellular response to hydrogen peroxide / cell migration / positive regulation of T cell activation / regulation of gene expression / protein phosphatase binding / cellular response to lipopolysaccharide / cell surface / plasma membrane
Similarity search - Function
Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. ...Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type substrate 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsNakaishi, A.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural insight into the specific interaction between murine SHPS-1/SIRP alpha and its ligand CD47
Authors: Nakaishi, A. / Hirose, M. / Yoshimura, M. / Oneyama, C. / Saito, K. / Kuki, N. / Matsuda, M. / Honma, N. / Ohnishi, H. / Matozaki, T. / Okada, M. / Nakagawa, A.
History
DepositionMay 2, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type substrate 1
B: Tyrosine-protein phosphatase non-receptor type substrate 1


Theoretical massNumber of molelcules
Total (without water)26,0272
Polymers26,0272
Non-polymers00
Water5,459303
1
A: Tyrosine-protein phosphatase non-receptor type substrate 1


Theoretical massNumber of molelcules
Total (without water)13,0141
Polymers13,0141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein phosphatase non-receptor type substrate 1


Theoretical massNumber of molelcules
Total (without water)13,0141
Polymers13,0141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.555, 57.670, 69.186
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 Tyrosine-protein phosphatase non-receptor type substrate 1 / SHP substrate 1 / SHPS-1 / Inhibitory receptor SHPS-1 / Signal- regulatory protein alpha-1 / Sirp- ...SHP substrate 1 / SHPS-1 / Inhibitory receptor SHPS-1 / Signal- regulatory protein alpha-1 / Sirp-alpha-1 / mSIRP-alpha1 / MyD-1 antigen / Brain Ig-like molecule with tyrosine-based activation motifs / Bit / p84 / CD172a antigen / SRC homology 2 domain-containing protein tyrosine phosphatase substrate 1


Mass: 13013.616 Da / Num. of mol.: 2 / Fragment: ligand-binidng domain, Ig-like V-type domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Shps1 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami B / References: UniProt: P97797
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 1.86 Å3/Da / Density % sol: 33.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 32% PEG 4000, 0.1M PIPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Apr 3, 2006 / Details: vertical focusing mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.4→39.75 Å / Num. obs: 39022 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 13.2 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 7.3
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.34 / Num. unique all: 5624 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→39.75 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.769 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19914 1954 5 %RANDOM
Rwork0.17425 ---
all0.17553 ---
obs0.17553 37007 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.984 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20 Å2
2--0.77 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.4→39.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1796 0 0 303 2099
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221842
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.041.972520
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8435241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.18724.02677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.00315309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.4781512
X-RAY DIFFRACTIONr_chiral_restr0.1370.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021400
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.2840
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.21310
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2227
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.268
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5351.51181
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.44721903
X-RAY DIFFRACTIONr_scbond_it3.3063740
X-RAY DIFFRACTIONr_scangle_it4.8014.5609
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 135 -
Rwork0.211 2699 -
obs--100 %

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