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- PDB-1fxk: CRYSTAL STRUCTURE OF ARCHAEAL PREFOLDIN (GIMC). -

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Basic information

Entry
Database: PDB / ID: 1fxk
TitleCRYSTAL STRUCTURE OF ARCHAEAL PREFOLDIN (GIMC).
Components
  • (PREFOLDIN) x 2
  • PROTEIN (PREFOLDIN)
KeywordsCHAPERONE / ARCHAEAL PROTEIN
Function / homology
Function and homology information


prefoldin complex / unfolded protein binding / protein folding / cytoplasm
Similarity search - Function
Prefoldin subunit beta / Helix Hairpins - #370 / Prefoldin beta-like / Prefoldin alpha-like / Prefoldin alpha subunit, archaea-type / Prefoldin subunit / Prefoldin subunit / Prefoldin / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Prefoldin subunit beta / Prefoldin subunit alpha
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsSiegert, R. / Scheufler, C. / Moarefi, I.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2000
Title: Structure of the molecular chaperone prefoldin: unique interaction of multiple coiled coil tentacles with unfolded proteins.
Authors: Siegert, R. / Leroux, M.R. / Scheufler, C. / Hartl, F.U. / Moarefi, I.
History
DepositionSep 26, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PREFOLDIN
B: PREFOLDIN
C: PROTEIN (PREFOLDIN)


Theoretical massNumber of molelcules
Total (without water)39,8863
Polymers39,8863
Non-polymers00
Water5,999333
1
A: PREFOLDIN
B: PREFOLDIN
C: PROTEIN (PREFOLDIN)

A: PREFOLDIN
B: PREFOLDIN
C: PROTEIN (PREFOLDIN)


Theoretical massNumber of molelcules
Total (without water)79,7726
Polymers79,7726
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_745-x+2,-y-1,z1
Buried area9490 Å2
ΔGint-48 kcal/mol
Surface area42840 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)72.850, 90.690, 78.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PREFOLDIN


Mass: 12725.708 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Production host: Escherichia coli (E. coli) / References: UniProt: O26774
#2: Protein PREFOLDIN


Mass: 12782.761 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Production host: Escherichia coli (E. coli) / References: UniProt: O26774
#3: Protein PROTEIN (PREFOLDIN)


Mass: 14377.448 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Production host: Escherichia coli (E. coli) / References: UniProt: O27646
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.27 Å3/Da / Density % sol: 62.33 %
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: vapor diffusion, hanging drop
Details: temperature was shifted to 4 degrees after one week of incubation
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
2800 mMsodium acetate1reservoir
320 %ethylene glycol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.92801
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92801 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / % possible obs: 99.6 % / Observed criterion σ(I): 3 / Biso Wilson estimate: 25.4 Å2 / Rsym value: 4.4 / Net I/σ(I): 24.5
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 6.5 / Rsym value: 18.8 / % possible all: 99.6
Reflection
*PLUS
Rmerge(I) obs: 0.044
Reflection shell
*PLUS
% possible obs: 99.6 % / Rmerge(I) obs: 0.188

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→19.84 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1976 8.4 %RANDOM
Rwork0.218 ---
obs0.218 23569 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.77 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 46.6 Å2
Baniso -1Baniso -2Baniso -3
1--4.69 Å20 Å20 Å2
2---1.51 Å20 Å2
3---6.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2754 0 0 333 3087
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.481.5
X-RAY DIFFRACTIONc_mcangle_it2.242
X-RAY DIFFRACTIONc_scbond_it3.422
X-RAY DIFFRACTIONc_scangle_it4.922.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.273 296 8 %
Rwork0.225 3399 -
obs--94.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77

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