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- PDB-1t1v: Crystal Structure of the Glutaredoxin-like Protein SH3BGRL3 at 1.... -

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Basic information

Entry
Database: PDB / ID: 1t1v
TitleCrystal Structure of the Glutaredoxin-like Protein SH3BGRL3 at 1.6 A resolution
ComponentsSH3 domain-binding glutamic acid-rich protein-like 3
KeywordsSIGNALING PROTEIN / GLUTAREDOXIN / THIOREDOXIN FOLD / PROTEIN 3D-STRUCTURE / X-RAY CRYSTALLOGRAPHY
Function / homology
Function and homology information


cytoskeleton organization / ruffle membrane / nuclear body / cytosol
Similarity search - Function
SH3-binding, glutamic acid-rich protein / : / SH3-binding, glutamic acid-rich protein / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / SH3 domain-binding glutamic acid-rich-like protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsNardini, M. / Mazzocco, M. / Massaro, M. / Maffei, M. / Vergano, A. / Donadini, A. / Scartezzini, M. / Bolognesi, M.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2004
Title: Crystal structure of the glutaredoxin-like protein SH3BGRL3 at 1.6 A resolution
Authors: Nardini, M. / Mazzocco, M. / Massaro, M. / Maffei, M. / Vergano, A. / Donadini, A. / Scartezzini, M. / Bolognesi, M.
History
DepositionApr 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 23, 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_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

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Assembly

Deposited unit
A: SH3 domain-binding glutamic acid-rich protein-like 3
B: SH3 domain-binding glutamic acid-rich protein-like 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3206
Polymers20,9752
Non-polymers3444
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.624, 80.380, 34.660
Angle α, β, γ (deg.)90.00, 93.96, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein SH3 domain-binding glutamic acid-rich protein-like 3 / SH3BGRL3


Mass: 10487.724 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q91VW3
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 1.97 Å3/Da / Density % sol: 36.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Ammonium sulfate, Na-acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 12, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.6→34.5 Å / Num. all: 21080 / Num. obs: 18915 / % possible obs: 99.4 % / Observed criterion σ(I): 0.5 / Rmerge(I) obs: 0.098 / Net I/σ(I): 13.1
Reflection shellResolution: 1.6→1.64 Å / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 5.3 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J0F

1j0f


Resolution: 1.6→34.5 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.12 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24426 2139 10.2 %RANDOM
Rwork0.19719 ---
all0.202 21080 --
obs0.20199 18915 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.205 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å20.9 Å2
2---2.08 Å20 Å2
3---2.77 Å2
Refinement stepCycle: LAST / Resolution: 1.6→34.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1468 0 20 140 1628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0211510
X-RAY DIFFRACTIONr_bond_other_d00.021355
X-RAY DIFFRACTIONr_angle_refined_deg2.0121.9762035
X-RAY DIFFRACTIONr_angle_other_deg3.82333169
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3135184
X-RAY DIFFRACTIONr_chiral_restr0.140.2228
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021666
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02282
X-RAY DIFFRACTIONr_nbd_refined0.2590.2465
X-RAY DIFFRACTIONr_nbd_other0.2870.21494
X-RAY DIFFRACTIONr_nbtor_other0.1070.2786
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.236
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2750.239
X-RAY DIFFRACTIONr_symmetry_vdw_other0.330.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0920.27
X-RAY DIFFRACTIONr_mcbond_it1.3031.5925
X-RAY DIFFRACTIONr_mcangle_it2.19621494
X-RAY DIFFRACTIONr_scbond_it3.493585
X-RAY DIFFRACTIONr_scangle_it5.4564.5541
LS refinement shellResolution: 1.6→1.645 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.292 140
Rwork0.252 1376

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