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- PDB-1t7s: Structural Genomics of Caenorhabditis elegans: Structure of BAG-1... -

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Basic information

Entry
Database: PDB / ID: 1t7s
TitleStructural Genomics of Caenorhabditis elegans: Structure of BAG-1 protein
ComponentsBAG-1 cochaperone
KeywordsCHAPERONE / Structural genomics / BAG-1 cochaperone / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG
Function / homology
Function and homology information


chaperone cofactor-dependent protein refolding / protein-folding chaperone binding
Similarity search - Function
Molecular chaperone regulator BAG-1 / 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 ...Molecular chaperone regulator BAG-1 / 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
BAG family molecular chaperone regulator 1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsSymersky, J. / Zhang, Y. / Schormann, N. / Li, S. / Bunzel, R. / Pruett, P. / Luan, C.-H. / Luo, M. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structural genomics of Caenorhabditis elegans: structure of the BAG domain.
Authors: Symersky, J. / Zhang, Y. / Schormann, N. / Li, S. / Bunzel, R. / Pruett, P. / Luan, C.H. / Luo, M.
History
DepositionMay 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BAG-1 cochaperone
B: BAG-1 cochaperone


Theoretical massNumber of molelcules
Total (without water)32,2952
Polymers32,2952
Non-polymers00
Water90150
1
A: BAG-1 cochaperone


Theoretical massNumber of molelcules
Total (without water)16,1481
Polymers16,1481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BAG-1 cochaperone


Theoretical massNumber of molelcules
Total (without water)16,1481
Polymers16,1481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: BAG-1 cochaperone

A: BAG-1 cochaperone


Theoretical massNumber of molelcules
Total (without water)32,2952
Polymers32,2952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y,-z1
Buried area5760 Å2
ΔGint-50 kcal/mol
Surface area16440 Å2
MethodPISA
4
B: BAG-1 cochaperone

B: BAG-1 cochaperone


Theoretical massNumber of molelcules
Total (without water)32,2952
Polymers32,2952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+11
Buried area5970 Å2
ΔGint-44 kcal/mol
Surface area16220 Å2
MethodPISA
5
B: BAG-1 cochaperone

B: BAG-1 cochaperone

B: BAG-1 cochaperone

B: BAG-1 cochaperone


Theoretical massNumber of molelcules
Total (without water)64,5914
Polymers64,5914
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_576x,-y+2,-z+11
Buried area14710 Å2
ΔGint-110 kcal/mol
Surface area29680 Å2
MethodPISA
6
A: BAG-1 cochaperone

A: BAG-1 cochaperone

A: BAG-1 cochaperone

A: BAG-1 cochaperone


Theoretical massNumber of molelcules
Total (without water)64,5914
Polymers64,5914
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
crystal symmetry operation3_755-x+2,y,-z1
crystal symmetry operation4_575x,-y+2,-z1
Buried area14440 Å2
ΔGint-117 kcal/mol
Surface area29960 Å2
MethodPISA
7
B: BAG-1 cochaperone

B: BAG-1 cochaperone


Theoretical massNumber of molelcules
Total (without water)32,2952
Polymers32,2952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
Buried area1230 Å2
ΔGint-10 kcal/mol
Surface area20960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.518, 86.164, 125.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein BAG-1 cochaperone / human BAG1 homolog / BCL-2 binding athanogene


Mass: 16147.665 Da / Num. of mol.: 2 / Fragment: residues 74-210 / Mutation: SeMET variant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: Bag-1 / Plasmid: PET28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI / References: UniProt: O44739
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 3.32 Å3/Da / Density % sol: 62.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 1.6M ammonium sulfate, 0.1M MES, 5% dioxane, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979244 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 17, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979244 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 19501 / Num. obs: 19481 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 3.9 % / Biso Wilson estimate: 64.7 Å2 / Rsym value: 0.068 / Net I/σ(I): 12.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 1034 / Rsym value: 0.314 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→37.63 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000 / 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
Rfree0.298 963 4.9 %RANDOM
Rwork0.224 ---
obs0.224 19481 99.9 %-
all-19501 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.06 Å2 / ksol: 0.351313 e/Å3
Displacement parametersBiso mean: 57.7 Å2
Baniso -1Baniso -2Baniso -3
1-10.12 Å20 Å20 Å2
2--2.67 Å20 Å2
3----12.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.8→37.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2108 0 0 50 2158
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d18.5
X-RAY DIFFRACTIONc_improper_angle_d0.66
X-RAY DIFFRACTIONc_mcbond_it5.651.5
X-RAY DIFFRACTIONc_mcangle_it8.262
X-RAY DIFFRACTIONc_scbond_it9.092
X-RAY DIFFRACTIONc_scangle_it12.312.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.401 188 5.8 %
Rwork0.332 3056 -
obs-3056 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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