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- PDB-1d1z: CRYSTAL STRUCTURE OF THE XLP PROTEIN SAP -

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Basic information

Entry
Database: PDB / ID: 1d1z
TitleCRYSTAL STRUCTURE OF THE XLP PROTEIN SAP
ComponentsSAP SH2 DOMAIN
KeywordsGENE REGULATION / SH2 DOMAINS
Function / homology
Function and homology information


positive regulation of natural killer cell mediated cytotoxicity / natural killer cell mediated cytotoxicity / negative regulation of T cell receptor signaling pathway / humoral immune response / regulation of immune response / cellular defense response / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell-cell signaling / adaptive immune response / cytosol / cytoplasm
Similarity search - Function
SH2 protein 1A / SH2D1A, SH2 domain / SH2 domain / SHC Adaptor Protein / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
SH2 domain-containing protein 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4 Å
AuthorsPoy, F. / Yaffe, M.B. / Sayos, J. / Saxena, K. / Eck, M.J.
Citation
Journal: Mol.Cell / Year: 1999
Title: Crystal structures of the XLP protein SAP reveal a class of SH2 domains with extended, phosphotyrosine-independent sequence recognition.
Authors: Poy, F. / Yaffe, M.B. / Sayos, J. / Saxena, K. / Morra, M. / Sumegi, J. / Cantley, L.C. / Terhorst, C. / Eck, M.J.
#1: Journal: Nature / Year: 1998
Title: The X-linked lymphoproliferative-disease gene product SAP regulates signals induced through the co-receptor SLAM
Authors: Sayos, J. / Wu, C. / Morra, M. / Wang, N. / Terhorst, C.
History
DepositionSep 22, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: SAP SH2 DOMAIN
B: SAP SH2 DOMAIN
C: SAP SH2 DOMAIN
D: SAP SH2 DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,48211
Polymers46,8104
Non-polymers6727
Water11,313628
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: SAP SH2 DOMAIN
hetero molecules

C: SAP SH2 DOMAIN
hetero molecules

B: SAP SH2 DOMAIN
D: SAP SH2 DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,48211
Polymers46,8104
Non-polymers6727
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation1_654x+1,y,z-11
crystal symmetry operation1_664x+1,y+1,z-11
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-147 kcal/mol
Surface area20010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.480, 62.270, 65.090
Angle α, β, γ (deg.)65.71, 78.67, 89.66
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
SAP SH2 DOMAIN


Mass: 11702.393 Da / Num. of mol.: 4 / Fragment: SAP SH2 DOMAIN (RESIDUES 1-104)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: O60880
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 628 / 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: 2.5 Å3/Da / Density % sol: 50.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1.64 M AMMONIUM SULFATE, 100 MM SODIUM CITRATE, PH 5.6, AND 10 MM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 22K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
220 mMHEPES1drop
3150 mM1dropNaCl
410 mMdithiothreitol1drop
51.64 Mammonium sulfate1reservoir
6100 mMsodium citrate1reservoir
710 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1
DetectorType: PRINCETON 2K / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.4→22 Å / Num. obs: 83110 / % possible obs: 92.9 % / Rmerge(I) obs: 0.062
Reflection
*PLUS
Num. measured all: 274082

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementResolution: 1.4→10 Å / σ(F): 4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.187 -RANDOM
Rwork0.139 --
all0.147 78862 -
obs0.139 78862 -
Refinement stepCycle: LAST / Resolution: 1.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3160 0 35 628 3823
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 10 Å / σ(F): 4
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.029

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