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- PDB-1u6t: Crystal structure of the human SH3 binding glutamic-rich protein like -

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Basic information

Entry
Database: PDB / ID: 1u6t
TitleCrystal structure of the human SH3 binding glutamic-rich protein like
ComponentsSH3 domain-binding glutamic acid-rich-like protein
KeywordsPROTEIN BINDING / SIGNALING PROTEIN / SH3-binding / GLUTAREDOXIN / THIOREDOXIN FOLD
Function / homology
Function and homology information


protein-RNA adaptor activity / positive regulation of cytoplasmic translational initiation / ubiquitin-like ligase-substrate adaptor activity / SH3 domain binding / proteasome-mediated ubiquitin-dependent protein catabolic process / extracellular space / extracellular exosome / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
SH3-binding, glutamic acid-rich protein / SH3-binding, glutamic acid-rich protein / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Adapter SH3BGRL
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 1.9 Å
AuthorsYin, L. / Xiang, Y. / Yang, N. / Zhu, D.-Y. / Huang, R.-H. / Wang, D.-C.
CitationJournal: Proteins / Year: 2005
Title: Crystal structure of human SH3BGRL protein: the first structure of the human SH3BGR family representing a novel class of thioredoxin fold proteins
Authors: Yin, L. / Xiang, Y. / Zhu, D.-Y. / Yan, N. / Huang, R.-H. / Zhang, Y. / Wang, D.-C.
History
DepositionAug 1, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 9, 2005Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: SH3 domain-binding glutamic acid-rich-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9202
Polymers13,7281
Non-polymers1921
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.886, 34.815, 97.965
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 SH3 domain-binding glutamic acid-rich-like protein / SH3 Binding Glutamic-rich Protein Like


Mass: 13728.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O75368
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 33.7876 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: tri-Sodium Citrate dihydrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 9, 2004
RadiationMonochromator: Confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→28.38 Å / Num. all: 8290 / Num. obs: 8126 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 18.781 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 9.1
Reflection shellResolution: 1.9→1.99 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 4.9 / Num. unique all: 856 / Rsym value: 0.12 / % possible all: 85.2

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXD& SHARPphasing
CNSrefinement
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.9→28.38 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.212 848 -random
Rwork0.168 ---
obs0.168 8126 98 %-
all-8290 --
Displacement parametersBiso mean: 16.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å21.27 Å2-0.86 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.9→28.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms978 0 13 192 1183
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_torsion_deg21.1
X-RAY DIFFRACTIONx_torsion_impr_deg0.7
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
1.9-1.990.307950.2350.03185685.2
1.99-2.090.239940.1780.025101199.7
2.09-2.220.207770.1720.0241029100

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