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- PDB-2aug: Crystal structure of the Grb14 SH2 domain -

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Basic information

Entry
Database: PDB / ID: 2aug
TitleCrystal structure of the Grb14 SH2 domain
ComponentsGrowth factor receptor-bound protein 14
KeywordsSIGNALING PROTEIN / Phosphorylation / SH2 domain
Function / homology
Function and homology information


Tie2 Signaling / negative regulation of insulin receptor signaling pathway / receptor tyrosine kinase binding / insulin receptor signaling pathway / protein-macromolecule adaptor activity / molecular adaptor activity / endosome membrane / intracellular membrane-bounded organelle / signal transduction / plasma membrane ...Tie2 Signaling / negative regulation of insulin receptor signaling pathway / receptor tyrosine kinase binding / insulin receptor signaling pathway / protein-macromolecule adaptor activity / molecular adaptor activity / endosome membrane / intracellular membrane-bounded organelle / signal transduction / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Grb14, SH2 domain / BPS (Between PH and SH2) domain / BPS (Between PH and SH2) / GRB/APBB1IP / APBB1IP, PH domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / SH2 domain ...Grb14, SH2 domain / BPS (Between PH and SH2) domain / BPS (Between PH and SH2) / GRB/APBB1IP / APBB1IP, PH domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / SH2 domain / SHC Adaptor Protein / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / PH-like domain superfamily / Ubiquitin-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Growth factor receptor-bound protein 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDepetris, R.S. / Hu, J. / Gimpelevich, I. / Holt, L.J. / Daly, R.J. / Hubbard, S.R.
CitationJournal: Mol.Cell / Year: 2005
Title: Structural basis for inhibition of the insulin receptor by the adaptor protein grb14.
Authors: Depetris, R.S. / Hu, J. / Gimpelevich, I. / Holt, L.J. / Daly, R.J. / Hubbard, S.R.
History
DepositionAug 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Growth factor receptor-bound protein 14
B: Growth factor receptor-bound protein 14


Theoretical massNumber of molelcules
Total (without water)29,2672
Polymers29,2672
Non-polymers00
Water2,810156
1
A: Growth factor receptor-bound protein 14

A: Growth factor receptor-bound protein 14


Theoretical massNumber of molelcules
Total (without water)29,2672
Polymers29,2672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
2
B: Growth factor receptor-bound protein 14

B: Growth factor receptor-bound protein 14


Theoretical massNumber of molelcules
Total (without water)29,2672
Polymers29,2672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Unit cell
Length a, b, c (Å)49.118, 49.118, 184.087
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Growth factor receptor-bound protein 14 / GRB14 adaptor protein


Mass: 14633.711 Da / Num. of mol.: 2 / Fragment: SH2 domain / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q14449
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.19 Å3/Da / Density % sol: 43.82 %
Description: BECAUSE OF THE MODEST RESOLUTION, THE ASSIGNMENT AND POSITIONS OF THE TWO CALCIUM IONS SHOULD BE CONSIDERED TENTATIVE.
Crystal growpH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 15, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→27.84 Å / Num. obs: 11856 / % possible obs: 99.7 % / Biso Wilson estimate: 13.2 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 14.2
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.166 / Mean I/σ(I) obs: 14.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NRV

1nrv


Resolution: 2.3→27.84 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 338462.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.248 609 5.1 %RANDOM
Rwork0.199 ---
obs-11856 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.0867 Å2 / ksol: 0.343598 e/Å3
Displacement parametersBiso mean: 16.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å21.48 Å20 Å2
2--0.62 Å20 Å2
3----1.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.3→27.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1745 0 0 156 1901
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.8741.5
X-RAY DIFFRACTIONc_mcangle_it1.5322
X-RAY DIFFRACTIONc_scbond_it1.1522
X-RAY DIFFRACTIONc_scangle_it1.8082.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.295 93 5 %
Rwork0.211 1783 -
obs--95.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4TOPPAR:paramcsdx.misc

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