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- PDB-3d0t: Structure of the BNB domain of the Hsp70 cochaperone Bag2 -

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Basic information

Entry
Database: PDB / ID: 3d0t
TitleStructure of the BNB domain of the Hsp70 cochaperone Bag2
ComponentsBAG family molecular chaperone regulator 2
KeywordsCHAPERONE / 4-helix bundle / Coiled coil
Function / homology
Function and homology information


Regulation of HSF1-mediated heat shock response / adenyl-nucleotide exchange factor activity / positive regulation of protein processing / positive regulation of proteasomal protein catabolic process / protein metabolic process / protein folding chaperone complex / negative regulation of protein ubiquitination / heat shock protein binding / tau protein binding / protein-folding chaperone binding ...Regulation of HSF1-mediated heat shock response / adenyl-nucleotide exchange factor activity / positive regulation of protein processing / positive regulation of proteasomal protein catabolic process / protein metabolic process / protein folding chaperone complex / negative regulation of protein ubiquitination / heat shock protein binding / tau protein binding / protein-folding chaperone binding / transmembrane transporter binding / protein stabilization / axon / ubiquitin protein ligase binding / dendrite / identical protein binding
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #890 / BAG family molecular chaperone regulator 2 / BAG domain / BAG domain profile. / BAG domains, present in regulator of Hsp70 proteins / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
BAG family molecular chaperone regulator 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.55 Å
AuthorsXu, Z. / Nix, J.C. / Devlin, K. / Misra, S.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Structural basis of nucleotide exchange and client binding by the Hsp70 cochaperone Bag2.
Authors: Xu, Z. / Page, R.C. / Gomes, M.M. / Kohli, E. / Nix, J.C. / Herr, A.B. / Patterson, C. / Misra, S.
History
DepositionMay 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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

Downloads & links

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Assembly

Deposited unit
A: BAG family molecular chaperone regulator 2
B: BAG family molecular chaperone regulator 2
C: BAG family molecular chaperone regulator 2
D: BAG family molecular chaperone regulator 2


Theoretical massNumber of molelcules
Total (without water)38,8044
Polymers38,8044
Non-polymers00
Water95553
1
C: BAG family molecular chaperone regulator 2
D: BAG family molecular chaperone regulator 2


Theoretical massNumber of molelcules
Total (without water)19,4022
Polymers19,4022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-31 kcal/mol
Surface area9220 Å2
MethodPISA
2
A: BAG family molecular chaperone regulator 2
B: BAG family molecular chaperone regulator 2


Theoretical massNumber of molelcules
Total (without water)19,4022
Polymers19,4022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-29 kcal/mol
Surface area9220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.680, 104.680, 164.300
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

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


Mass: 9701.124 Da / Num. of mol.: 4 / Fragment: Bag-like domain (UNP residues 107-189)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bag2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q91YN9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.14 Å3/Da / Density % sol: 42.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 35% PEG 400, 0.1M Bis-Tris pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.96410908, 0.99505962
DetectorType: NOIR-1 / Detector: CCD / Date: Feb 10, 2007 / Details: beamline
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.964109081
20.995059621
ReflectionRedundancy: 17.5 % / Av σ(I) over netI: 8.7 / Number: 208914 / Rmerge(I) obs: 0.1 / Χ2: 1.33 / D res high: 2.4 Å / D res low: 30 Å / Num. obs: 11934 / % possible obs: 84.5
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)% possible obs (%)Rmerge(I) obsChi squaredRedundancyRejects
5.16301000.0642.90120.4120
4.15.1699.90.0791.7920.965
3.584.199.90.0981.4621.141
3.263.5899.90.1251.08319.935
3.023.2696.50.160.8471835
2.853.0286.20.1930.75116.630
2.72.8578.90.2390.61415.252
2.592.769.90.2520.55113.261
2.492.5958.20.2760.49411.837
2.42.4953.30.3290.4859.638
ReflectionResolution: 2.55→52.34 Å / Num. all: 11539 / Num. obs: 11398 / % possible obs: 98.8 % / Observed criterion σ(I): 5 / Redundancy: 5.96 % / Rmerge(I) obs: 0.059 / Χ2: 0.98 / Net I/σ(I): 14.5 / Scaling rejects: 514
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 5.92 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 5.7 / Num. measured all: 6731 / Num. unique all: 1131 / Χ2: 1.17 / % possible all: 99.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
CNS1.1refinement
PDB_EXTRACT3.005data extraction
d*TREKdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.55→39.69 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 453570.875 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 583 5.2 %RANDOM
Rwork0.253 ---
all-11549 --
obs-11295 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.615 Å2 / ksol: 0.383 e/Å3
Displacement parametersBiso mean: 54.6 Å2
Baniso -1Baniso -2Baniso -3
1--6.28 Å22.82 Å20 Å2
2---6.28 Å20 Å2
3---12.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.55→39.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2430 0 0 53 2483
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d16.3
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.55→2.64 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.37 60 5.4 %
Rwork0.266 1056 -
all-1116 -
obs-1112 98.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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