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- PDB-4hwh: Crystal structure of ATBAG4 -

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Basic information

Entry
Database: PDB / ID: 4hwh
TitleCrystal structure of ATBAG4
ComponentsBAG family molecular chaperone regulator 4
KeywordsAPOPTOSIS / three helix bundle / co-chaperone
Function / homology
Function and homology information


vegetative to reproductive phase transition of meristem / regulation of stomatal movement / positive regulation of potassium ion transport / protein targeting to membrane / endoplasmic reticulum exit site / response to salt stress / response to cold / protein-folding chaperone binding / endoplasmic reticulum / cytosol
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 family / Ubiquitin domain profile. ...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 family / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / MALONIC ACID / BAG family molecular chaperone regulator 4
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.895 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 1.2Apr 29, 2015Group: Non-polymer description
Revision 1.3Feb 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

Downloads & links

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Assembly

Deposited unit
A: BAG family molecular chaperone regulator 4
B: BAG family molecular chaperone regulator 4
C: BAG family molecular chaperone regulator 4
D: BAG family molecular chaperone regulator 4
E: BAG family molecular chaperone regulator 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,04112
Polymers47,5055
Non-polymers5367
Water4,702261
1
A: BAG family molecular chaperone regulator 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6643
Polymers9,5011
Non-polymers1632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BAG family molecular chaperone regulator 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5932
Polymers9,5011
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: BAG family molecular chaperone regulator 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6643
Polymers9,5011
Non-polymers1632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: BAG family molecular chaperone regulator 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5602
Polymers9,5011
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: BAG family molecular chaperone regulator 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5602
Polymers9,5011
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.663, 73.328, 111.634
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 4 / Bcl-2-associated athanogene 4


Mass: 9500.955 Da / Num. of mol.: 5 / Fragment: BAG domain (UNP residues 138-223)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At3g51780, atbag4, ATEM1.3, BAG4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RX71
#2: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O4
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.74 Å3/Da / Density % sol: 55.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 10% tascimate, 20% PEG3350, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 / Wavelength: 0.9795 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 wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.895→24.189 Å / Num. all: 42458 / Num. obs: 40074 / % possible obs: 95.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.895→1.94 Å / % possible all: 72.1

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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: 1.895→24.189 Å / SU ML: 0.21 / σ(F): 0 / Phase error: 24.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2358 1954 5.06 %
Rwork0.2069 --
obs0.2084 38621 91.55 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.781 Å2 / ksol: 0.376 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.5595 Å20 Å2-0 Å2
2--9.6645 Å20 Å2
3----4.105 Å2
Refinement stepCycle: LAST / Resolution: 1.895→24.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3254 0 36 261 3551
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053281
X-RAY DIFFRACTIONf_angle_d0.6094383
X-RAY DIFFRACTIONf_dihedral_angle_d14.3711254
X-RAY DIFFRACTIONf_chiral_restr0.035540
X-RAY DIFFRACTIONf_plane_restr0.001580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.895-1.94290.265970.24391632X-RAY DIFFRACTION58
1.9429-1.99540.3119980.23782046X-RAY DIFFRACTION72
1.9954-2.0540.28011510.23892313X-RAY DIFFRACTION83
2.054-2.12030.25431380.2232518X-RAY DIFFRACTION89
2.1203-2.1960.26611270.20862621X-RAY DIFFRACTION92
2.196-2.28390.211480.2052679X-RAY DIFFRACTION95
2.2839-2.38780.25141420.20192764X-RAY DIFFRACTION97
2.3878-2.51350.27971390.21042771X-RAY DIFFRACTION98
2.5135-2.67080.28471390.2162834X-RAY DIFFRACTION98
2.6708-2.87670.27391350.22492821X-RAY DIFFRACTION99
2.8767-3.16570.24881520.21422854X-RAY DIFFRACTION99
3.1657-3.62240.22461590.19922875X-RAY DIFFRACTION100
3.6224-4.55890.19571510.18152929X-RAY DIFFRACTION100
4.5589-24.19080.21211780.20933010X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 3.0495 Å / Origin y: -15.3168 Å / Origin z: -17.3861 Å
111213212223313233
T0.1452 Å20.0299 Å20.0084 Å2-0.1143 Å20.0151 Å2--0.1338 Å2
L0.9468 °20.4521 °2-0.0013 °2-0.2688 °20.133 °2--0.308 °2
S-0.0719 Å °0.134 Å °0.078 Å °-0.0575 Å °0.0561 Å °0.0319 Å °-0.0277 Å °-0.0303 Å °0.0126 Å °
Refinement TLS groupSelection details: all

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