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- PDB-2zqm: Crystal structure of the prefoldin beta subunit from Thermococcus... -

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Basic information

Entry
Database: PDB / ID: 2zqm
TitleCrystal structure of the prefoldin beta subunit from Thermococcus strain KS-1
ComponentsPrefoldin beta subunit 1
KeywordsCHAPERONE / PREFOLDIN
Function / homology
Function and homology information


prefoldin complex / protein folding chaperone / unfolded protein binding / cytoplasm
Similarity search - Function
Prefoldin subunit beta / Helix Hairpins - #370 / Prefoldin beta-like / Prefoldin subunit / Prefoldin / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CITRIC ACID / Prefoldin subunit beta
Similarity search - Component
Biological speciesThermococcus sp. (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å
AuthorsKida, H. / Miki, K.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural and molecular characterization of the prefoldin beta subunit from Thermococcus strain KS-1
Authors: Kida, H. / Sugano, Y. / Iizuka, R. / Fujihashi, M. / Yohda, M. / Miki, K.
History
DepositionAug 13, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / 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 / pdbx_struct_special_symmetry / 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 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8617
Polymers13,2081
Non-polymers6536
Water2,522140
1
A: Prefoldin beta subunit 1
hetero molecules

A: Prefoldin beta subunit 1
hetero molecules

A: Prefoldin beta subunit 1
hetero molecules

A: Prefoldin beta subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,44328
Polymers52,8334
Non-polymers2,61024
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area7880 Å2
ΔGint-28 kcal/mol
Surface area31390 Å2
MethodPISA
2
A: Prefoldin beta subunit 1
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)110,88756
Polymers105,6668
Non-polymers5,22148
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_556-x,y,-z+11
crystal symmetry operation6_556x,-y,-z+11
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_556-y,-x,-z+11
Buried area28580 Å2
ΔGint-92 kcal/mol
Surface area49960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.603, 70.603, 114.421
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-309-

GOL

21A-309-

GOL

31A-310-

HOH

41A-311-

HOH

51A-312-

HOH

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Components

#1: Protein Prefoldin beta subunit 1


Mass: 13208.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus sp. (archaea) / Strain: KS-1 / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / References: UniProt: B0I3E0
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.7 Å3/Da / Density % sol: 54.43 %
Crystal growTemperature: 291 K / pH: 4.2
Details: 25% (v/v) 1,2-propanediol, phosphate-citrate pH 4.2, 5% (v/v) PEG 3000, 5% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 6, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 11352 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 13.6 Å2 / Rsym value: 0.038 / Net I/σ(I): 43.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 6.3 / Rsym value: 0.16 / % possible all: 93.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIR / Resolution: 1.9→49.92 Å / Rfactor Rfree error: 0.008 / Occupancy max: 1 / Occupancy min: 0.25 / Data cutoff high absF: 1981634.97 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.194 540 4.9 %RANDOM
Rwork0.178 ---
obs0.178 10978 93.2 %-
all-10978 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.2159 Å2 / ksol: 0.374319 e/Å3
Displacement parametersBiso mean: 26.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.44 Å20 Å20 Å2
2--3.44 Å20 Å2
3----6.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.9→49.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms904 0 43 140 1087
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d5.34
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.6991.5
X-RAY DIFFRACTIONc_mcangle_it3.2922
X-RAY DIFFRACTIONc_scbond_it4.8692
X-RAY DIFFRACTIONc_scangle_it6.7562.5
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.26 51 5.2 %
Rwork0.23 935 -
obs--86 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4ligand.param

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