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- PDB-4hwd: Crystal structure of ATBAG2 -

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Basic information

Entry
Database: PDB / ID: 4hwd
TitleCrystal structure of ATBAG2
ComponentsBAG family molecular chaperone regulator 2
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 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.312 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
D: BAG family molecular chaperone regulator 2
A: BAG family molecular chaperone regulator 2
B: BAG family molecular chaperone regulator 2


Theoretical massNumber of molelcules
Total (without water)29,7613
Polymers29,7613
Non-polymers00
Water3,279182
1
D: BAG family molecular chaperone regulator 2


Theoretical massNumber of molelcules
Total (without water)9,9201
Polymers9,9201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: BAG family molecular chaperone regulator 2


Theoretical massNumber of molelcules
Total (without water)9,9201
Polymers9,9201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: BAG family molecular chaperone regulator 2


Theoretical massNumber of molelcules
Total (without water)9,9201
Polymers9,9201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)26.136, 60.452, 177.034
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 BAG family molecular chaperone regulator 2 / Bcl-2-associated athanogene 2


Mass: 9920.485 Da / Num. of mol.: 3 / Fragment: BAG domain (UNP residues 129-214)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g62100, BAG2, MTG10.13 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0WPX7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.35 Å3/Da / Density % sol: 47.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M ammonium sulfate, 20% PEG3350, 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: 0.9793 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Feb 3, 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
20.97931
ReflectionResolution: 2.312→35.711 Å / Num. all: 13096 / Num. obs: 12982 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.312→2.35 Å / % possible all: 95.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(PHENIX.REFINE)model building
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.312→35.711 Å / SU ML: 0.25 / σ(F): 0 / Phase error: 22.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2532 636 4.92 %
Rwork0.2305 --
obs0.2316 12931 98.88 %
all-13030 -
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.304 Å2 / ksol: 0.351 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.8223 Å2-0 Å20 Å2
2---7.4584 Å2-0 Å2
3---4.6361 Å2
Refinement stepCycle: LAST / Resolution: 2.312→35.711 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2023 0 0 182 2205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062032
X-RAY DIFFRACTIONf_angle_d0.9842700
X-RAY DIFFRACTIONf_dihedral_angle_d16.07808
X-RAY DIFFRACTIONf_chiral_restr0.08314
X-RAY DIFFRACTIONf_plane_restr0.003342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.312-2.49050.31481220.24572322X-RAY DIFFRACTION96
2.4905-2.74110.2971350.25222423X-RAY DIFFRACTION99
2.7411-3.13750.261320.24872415X-RAY DIFFRACTION99
3.1375-3.95210.24141110.22992503X-RAY DIFFRACTION100
3.9521-35.71510.20721360.20162632X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -11.6405 Å / Origin y: -2.0873 Å / Origin z: 23.6578 Å
111213212223313233
T0.0196 Å2-0.0163 Å2-0.0066 Å2-0.0223 Å2-0.0134 Å2--0.0207 Å2
L0.0207 °20.0079 °2-0.0245 °2-0.0548 °2-0.048 °2--0.0565 °2
S-0.0091 Å °0.0311 Å °-0.0136 Å °0.0138 Å °0.018 Å °-0.026 Å °-0.0079 Å °-0.0342 Å °0.0134 Å °
Refinement TLS groupSelection details: all

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