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- PDB-4hwf: Crystal structure of ATBAG3 -

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Basic information

Entry
Database: PDB / ID: 4hwf
TitleCrystal structure of ATBAG3
ComponentsBAG family molecular chaperone regulator 3
KeywordsAPOPTOSIS / three helix bundle / co-chaperone
Function / homology
Function and homology information


protein-folding chaperone binding
Similarity search - Function
BAG domain / BAG domain superfamily / Molecular chaperone regulator BAG / BAG domain / BAG domain / BAG domain profile. / BAG domains, present in regulator of Hsp70 proteins / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Ubiquitin domain profile. / Ubiquitin-like domain ...BAG domain / BAG domain superfamily / Molecular chaperone regulator BAG / BAG domain / BAG domain / BAG domain profile. / BAG domains, present in regulator of Hsp70 proteins / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
BAG family molecular chaperone regulator 3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsShen, Y. / Fang, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structural insight into plant programmed cell death mediated by BAG proteins in Arabidopsis thaliana.
Authors: Fang, S. / Li, L. / Cui, B. / Men, S. / Shen, Y. / Yang, X.
History
DepositionNov 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Feb 28, 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

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Assembly

Deposited unit
A: BAG family molecular chaperone regulator 3
B: BAG family molecular chaperone regulator 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7494
Polymers19,5572
Non-polymers1922
Water2,540141
1
A: BAG family molecular chaperone regulator 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8742
Polymers9,7781
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BAG family molecular chaperone regulator 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8742
Polymers9,7781
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-58 kcal/mol
Surface area10860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.807, 55.807, 173.516
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein BAG family molecular chaperone regulator 3 / Bcl-2-associated athanogene 3


Mass: 9778.419 Da / Num. of mol.: 2 / Fragment: BAG domain (UNP residues 135-220)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g07220, BAG3, T28J14_160 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LYP4
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 3.97 Å3/Da / Density % sol: 69.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES sodium, 1.7 M lithium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 / Wavelength: 0.9794 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 10, 2010
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97941
ReflectionResolution: 2→32.283 Å / Num. all: 21456 / Num. obs: 21455 / % possible obs: 97.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellHighest resolution: 2 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→32.283 Å / SU ML: 0.2 / σ(F): 1.55 / Phase error: 21.92 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2445 1996 9.3 %
Rwork0.2178 --
obs0.2203 21455 97.45 %
all-21456 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.457 Å2 / ksol: 0.337 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.7828 Å20 Å20 Å2
2---1.7828 Å2-0 Å2
3---1.7249 Å2
Refinement stepCycle: LAST / Resolution: 2→32.283 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1258 0 10 141 1409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081271
X-RAY DIFFRACTIONf_angle_d0.8411701
X-RAY DIFFRACTIONf_dihedral_angle_d13.917493
X-RAY DIFFRACTIONf_chiral_restr0.056208
X-RAY DIFFRACTIONf_plane_restr0.003213
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05020.30141260.28111246X-RAY DIFFRACTION89
2.0502-2.10570.25521380.24191330X-RAY DIFFRACTION95
2.1057-2.16760.23871360.22341325X-RAY DIFFRACTION95
2.1676-2.23760.25311410.20941365X-RAY DIFFRACTION96
2.2376-2.31750.25121390.20491359X-RAY DIFFRACTION97
2.3175-2.41030.24211410.20131356X-RAY DIFFRACTION98
2.4103-2.51990.2391290.2171392X-RAY DIFFRACTION98
2.5199-2.65270.23251460.21771404X-RAY DIFFRACTION98
2.6527-2.81880.25811380.2271379X-RAY DIFFRACTION99
2.8188-3.03630.25411470.23011410X-RAY DIFFRACTION99
3.0363-3.34160.24031490.21231418X-RAY DIFFRACTION99
3.3416-3.82450.22311510.20541444X-RAY DIFFRACTION100
3.8245-4.81590.21151540.20191473X-RAY DIFFRACTION100
4.8159-32.28680.28011610.23191559X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 10.4859 Å / Origin y: 17.9531 Å / Origin z: 67.2494 Å
111213212223313233
T0.0131 Å2-0.0647 Å2-0.0182 Å2-0.1368 Å2-0.0569 Å2--0.0259 Å2
L0.0655 °20.0544 °20.1059 °2-0.0542 °20.0805 °2--0.3062 °2
S0.016 Å °0.0193 Å °-0.0316 Å °0.0162 Å °0.0335 Å °-0.0268 Å °-0.0278 Å °0.2091 Å °-0.07 Å °
Refinement TLS groupSelection details: all

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