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- PDB-3aei: Crystal structure of the prefoldin beta2 subunit from Thermococcu... -

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Basic information

Entry
Database: PDB / ID: 3aei
TitleCrystal structure of the prefoldin beta2 subunit from Thermococcus strain KS-1
ComponentsPrefoldin beta subunit 2
KeywordsCHAPERONE / double helix / coiled coil
Function / homology
Function and homology information


prefoldin complex / unfolded protein binding / protein folding
Similarity search - Function
Helix Hairpins - #370 / Prefoldin beta-like / Prefoldin subunit / Prefoldin / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Prefoldin beta subunit 2
Similarity search - Component
Biological speciesThermococcus sp. (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsOhtaki, A. / Sugano, Y. / Sato, T. / Noguchi, K. / Miyatake, H. / Yohda, M.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Thermodynamic Characterization of the Interaction between Prefoldin and Group II Chaperonin
Authors: Sahlan, M. / Zako, T. / Tai, P.T. / Ohtaki, A. / Noguchi, K. / Maeda, M. / Miyatake, H. / Dohmae, N. / Yohda, M.
History
DepositionFeb 8, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Prefoldin beta subunit 2
B: Prefoldin beta subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2828
Polymers23,8882
Non-polymers3956
Water2,630146
1
A: Prefoldin beta subunit 2
hetero molecules

A: Prefoldin beta subunit 2
hetero molecules

A: Prefoldin beta subunit 2
hetero molecules

A: Prefoldin beta subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,30212
Polymers47,7764
Non-polymers5268
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area5630 Å2
ΔGint-29 kcal/mol
Surface area24090 Å2
MethodPISA
2
B: Prefoldin beta subunit 2
hetero molecules

B: Prefoldin beta subunit 2
hetero molecules

B: Prefoldin beta subunit 2
hetero molecules

B: Prefoldin beta subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,82820
Polymers47,7764
Non-polymers1,05216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area5310 Å2
ΔGint-26 kcal/mol
Surface area24380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.315, 67.315, 92.415
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-101-

CL

21B-102-

CL

31A-143-

HOH

41A-144-

HOH

51B-122-

HOH

61B-173-

HOH

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Components

#1: Protein Prefoldin beta subunit 2


Mass: 11943.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus sp. (archaea) / Strain: KS-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: B0I3E2
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.19 Å3/Da / Density % sol: 43.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 500mM ammonium sulfate, 500mM ammonium chloride, 100mM sodium citrate pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1951
2951
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory AR-NW12A11
SYNCHROTRONSPring-8 BL38B121.13977
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDNov 17, 2007
MARMOSAIC 225 mm CCD2CCDOct 1, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.139771
ReflectionResolution: 1.7→50 Å / Num. obs: 24056 / Biso Wilson estimate: 26.4 Å2 / Num. measured all: 307371

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.7→33.66 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 0.25 / Data cutoff high absF: 203107.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1144 4.9 %RANDOM
Rwork0.21 ---
obs0.21 23582 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.903 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 88.71 Å2 / Biso mean: 30.9 Å2 / Biso min: 1.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2--0.67 Å20 Å2
3----1.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.7→33.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1596 0 18 146 1760
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.411.5
X-RAY DIFFRACTIONc_mcangle_it4.652
X-RAY DIFFRACTIONc_scbond_it6.442
X-RAY DIFFRACTIONc_scangle_it8.822.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.281 176 4.8 %
Rwork0.242 3526 -
all-3702 -
obs--94.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramprotein_rep.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4water_rep.top

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