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- PDB-2zdi: Crystal structure of Prefoldin from Pyrococcus horikoshii OT3 -

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Basic information

Entry
Database: PDB / ID: 2zdi
TitleCrystal structure of Prefoldin from Pyrococcus horikoshii OT3
Components
  • Prefoldin subunit alpha
  • Prefoldin subunit beta
KeywordsCHAPERONE / PREFOLDIN / Cytoplasm
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 alpha / Prefoldin subunit beta
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKida, H. / Miki, K.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structure and molecular dynamics simulation of archaeal prefoldin: the molecular mechanism for binding and recognition of nonnative substrate proteins
Authors: Ohtaki, A. / Kida, H. / Miyata, Y. / Ide, N. / Yonezawa, A. / Arakawa, T. / Iizuka, R. / Noguchi, K. / Kita, A. / Odaka, M. / Miki, K. / Yohda, M.
History
DepositionNov 23, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: Prefoldin subunit beta
B: Prefoldin subunit beta
C: Prefoldin subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9836
Polymers43,6943
Non-polymers2883
Water00
1
A: Prefoldin subunit beta
B: Prefoldin subunit beta
C: Prefoldin subunit alpha
hetero molecules

A: Prefoldin subunit beta
B: Prefoldin subunit beta
C: Prefoldin subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,96512
Polymers87,3896
Non-polymers5766
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area10300 Å2
ΔGint-107.9 kcal/mol
Surface area42230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.173, 98.750, 78.615
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 subunit beta / GimC subunit beta


Mass: 13333.361 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: pfdB / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / References: UniProt: O58268
#2: Protein Prefoldin subunit alpha / GimC subunit alpha


Mass: 17027.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: pfdA / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / References: UniProt: O58263
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
Sequence detailsTHE N-TERMINAL 3 RESIDUES (MET, ILE, ARG) OF CHAIN C (ENTITY 2) WERE INCLUDED IN ACCESSION NO. ...THE N-TERMINAL 3 RESIDUES (MET, ILE, ARG) OF CHAIN C (ENTITY 2) WERE INCLUDED IN ACCESSION NO. BA000001-547 OF DDBJ DATABASE, BUT NOT IN ACCESSION NO. O58263 OF UNIPROT DATABASE.

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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: 2.89 Å3/Da / Density % sol: 57.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% PEG 400, 0.1M Sodium chloride, 0.1M Lithium sulfate, 0.1M MES-NaOH pH6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 25, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 10215 / % possible obs: 94.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 66.56 Å2 / Rsym value: 0.055 / Net I/σ(I): 25.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREP9.4.09phasing
PHENIX1.24.1brefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FXK

1fxk


Resolution: 3→50 Å / Cross valid method: THROUGHOUT / σ(I): -3
RfactorNum. reflection% reflectionSelection details
Rfree0.277 478 -RANDOM
Rwork0.24 ---
obs-9874 92.7 %-
Displacement parametersBiso mean: 59.14 Å2
Baniso -1Baniso -2Baniso -3
1-17.36 Å20 Å20 Å2
2--29.01 Å20 Å2
3---26.84 Å2
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2651 0 15 0 2666

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