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- PDB-1mnf: Domain motions in GroEL upon binding of an oligopeptide -

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Basic information

Entry
Database: PDB / ID: 1mnf
TitleDomain motions in GroEL upon binding of an oligopeptide
Components
  • 12-residue peptide substrate
  • groEL proteinGroEL
KeywordsCHAPERONE / GROEL / FORCED UNFOLDING / DOMAIN MOTIONS / OPPOSITE ALLOSTERIC
Function / homology
Function and homology information


GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / response to heat ...GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / response to heat / protein refolding / magnesium ion binding / ATP hydrolysis activity / ATP binding / membrane / identical protein binding / cytosol
Similarity search - Function
GROEL; domain 2 / TCP-1-like chaperonin intermediate domain / GROEL; domain 1 / GroEL-like equatorial domain / GroEL / GroEL / Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily ...GROEL; domain 2 / TCP-1-like chaperonin intermediate domain / GROEL; domain 1 / GroEL-like equatorial domain / GroEL / GroEL / Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family / 3-Layer(bba) Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsWang, J. / Chen, L.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Domain Motions in GroEL upon Binding of an Oligopeptide.
Authors: Wang, J. / Chen, L.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1999
Title: The Crystal Structure of a Groel/Peptide Complex: Plasticity as a Basis for Substrate Diversity
Authors: Chen, L. / Sigler, P.B.
#2: Journal: Nat.Struct.Biol. / Year: 1996
Title: The 2.4 A Crystal Structure of the Bacterial Chaperonin Groel Complexed with ATP Gamma S
Authors: Boisvert, D.C. / Wang, J. / Otwinowski, Z. / Horwich, A.L. / Sigler, P.B.
#3: Journal: Nature / Year: 1994
Title: The Crystal Structure of the Bacterial Chaperonin Groel at 2.8 A
Authors: Braig, K. / Otwinowski, Z. / Hegde, R. / Boisvert, D.C. / Joachimiak, A. / Horwich, A.L. / Sigler, P.B.
#4: Journal: Nat.Struct.Biol. / Year: 1995
Title: Conformational Variability in the Refined Structure of the Chaperonin Groel at 2.8 A Resolution
Authors: Braig, K. / Adams, P.D. / Brunger, A.T.
#5: Journal: Nature / Year: 1997
Title: The Crystal Structure of the Asymmetric Groel-Groes-(Adp)7 Chaperonin Complex
Authors: Xu, Z. / Horwich, A.L. / Sigler, P.B.
History
DepositionSep 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: groEL protein
O: 12-residue peptide substrate
B: groEL protein
P: 12-residue peptide substrate
C: groEL protein
Q: 12-residue peptide substrate
D: groEL protein
R: 12-residue peptide substrate
E: groEL protein
S: 12-residue peptide substrate
F: groEL protein
T: 12-residue peptide substrate
G: groEL protein
U: 12-residue peptide substrate
H: groEL protein
V: 12-residue peptide substrate
I: groEL protein
W: 12-residue peptide substrate
J: groEL protein
X: 12-residue peptide substrate
K: groEL protein
Y: 12-residue peptide substrate
L: groEL protein
Z: 12-residue peptide substrate
M: groEL protein
1: 12-residue peptide substrate
N: groEL protein
2: 12-residue peptide substrate


Theoretical massNumber of molelcules
Total (without water)822,09728
Polymers822,09728
Non-polymers00
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70410 Å2
ΔGint-337 kcal/mol
Surface area287650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.415, 260.694, 148.691
Angle α, β, γ (deg.)90.00, 100.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
groEL protein / GroEL / Protein Cpn60 / groEL protein / AMS


Mass: 57260.504 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6F5
#2: Protein/peptide
12-residue peptide substrate / SBP / Strong Binding Peptide


Mass: 1460.676 Da / Num. of mol.: 14 / Source method: obtained synthetically / Details: The peptide was chemically synthesized.
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.75 %
Crystal growTemperature: 300 K / Method: vapor diffusion / pH: 7 / Details: PEG, pH 7, VAPOR DIFFUSION, temperature 300K
Crystal grow
*PLUS
Temperature: 28 ℃ / pH: 7 / Method: vapor diffusion, hanging drop / Details: Boisvert, D.C., (1996) Nat.Struct.Biol., 3, 170.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 mg/mlprotein1drop
22.2 %(w/v)PEG80001reservoir
325 mMBis-Tris-propane1reservoirpH7.0
415 %ethylene glycol1reservoir
55 %glycerol1reservoir
62.5 mM1reservoirMgCl2
750 mM1reservoirKCl
89 mM1reservoirCaCl2
100.01 %sodium azide1reservoir
91reservoir

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 20 Å / Num. obs: 167654 / % possible obs: 84.4 % / Num. measured all: 436111 / Rmerge(I) obs: 0.099
Reflection shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.2 Å / % possible obs: 73.9 % / Rmerge(I) obs: 0.147

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→20.01 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.259 16677 9.9 %RANDOM
Rwork0.236 ---
obs0.236 167654 83.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 16.633 Å2 / ksol: 0.326259 e/Å3
Displacement parametersBiso mean: 39.3 Å2
Baniso -1Baniso -2Baniso -3
1--12.35 Å20 Å24.62 Å2
2---12.91 Å20 Å2
3---25.27 Å2
Refine analyzeLuzzati coordinate error free: 0.42 Å / Luzzati sigma a free: 0.41 Å
Refinement stepCycle: LAST / Resolution: 3→20.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms55552 0 0 213 55765
Refine LS restraints
Refine-IDTypeDev ideal
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_d20.7
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_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.322 2484 9.8 %
Rwork0.304 22811 -
obs--75.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAM
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77
LS refinement shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.2 Å

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