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- PDB-4hel: Crystal structure analysis of apo-GroEL structure -

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Basic information

Entry
Database: PDB / ID: 4hel
TitleCrystal structure analysis of apo-GroEL structure
Components60 kDa chaperonin 4
KeywordsCHAPERONE / GroEL / Assist in protein folding / GroES
Function / homology
Function and homology information


chaperonin ATPase / isomerase activity / ATP-dependent protein folding chaperone / unfolded protein binding / protein refolding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
GROEL; domain 1 / GroEL-like equatorial domain / GROEL; domain 2 / TCP-1-like chaperonin intermediate domain / GroEL / GroEL / Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily ...GROEL; domain 1 / GroEL-like equatorial domain / GROEL; domain 2 / TCP-1-like chaperonin intermediate 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsSaxena, A.K. / Meena, S.R.
CitationJournal: To be Published
Title: Crystal structure of apo-GroEL structure
Authors: Meena, S.R. / Saxena, A.K.
History
DepositionOct 4, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 60 kDa chaperonin 4
B: 60 kDa chaperonin 4
C: 60 kDa chaperonin 4
D: 60 kDa chaperonin 4
E: 60 kDa chaperonin 4
F: 60 kDa chaperonin 4
G: 60 kDa chaperonin 4
H: 60 kDa chaperonin 4
I: 60 kDa chaperonin 4
J: 60 kDa chaperonin 4
K: 60 kDa chaperonin 4
L: 60 kDa chaperonin 4
M: 60 kDa chaperonin 4
N: 60 kDa chaperonin 4


Theoretical massNumber of molelcules
Total (without water)774,89014
Polymers774,89014
Non-polymers00
Water16,232901
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50490 Å2
ΔGint-218 kcal/mol
Surface area292470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.240, 261.830, 282.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
60 kDa chaperonin 4 / GroEL protein 4 / Protein Cpn60 4


Mass: 55349.285 Da / Num. of mol.: 14 / Fragment: GroEL fragment, UNP residues 2-526 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: Q548M1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 901 / 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: 3.25 Å3/Da / Density % sol: 62.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 32% MPD, 100mM Tris-HCl, 160mM MgCl2, 10% Glycerol, 2%(w/v) PEG6000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97327 Å
DetectorType: MARCCD225 / Detector: CCD / Date: Nov 9, 2011
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97327 Å / Relative weight: 1
ReflectionResolution: 3.2→59.4 Å / Num. all: 1247571 / Num. obs: 166588 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 56.9 Å2 / Rmerge(I) obs: 0.32 / Net I/σ(I): 6.1
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 2.4 / Num. unique all: 24106 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KP8

1kp8


Resolution: 3.2→59.38 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.887 / SU B: 16.859 / SU ML: 0.292 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.429 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22333 8354 5 %RANDOM
Rwork0.19799 ---
all0.19927 166588 --
obs0.19927 158133 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.395 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2---0.36 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 3.2→59.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms54096 0 0 901 54997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02254488
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.98873556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.81157336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.89826.0672100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.4481510136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.02615308
X-RAY DIFFRACTIONr_chiral_restr0.0850.28946
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02139550
X-RAY DIFFRACTIONr_mcbond_it4.071.536232
X-RAY DIFFRACTIONr_mcangle_it6.821257988
X-RAY DIFFRACTIONr_scbond_it7.423318256
X-RAY DIFFRACTIONr_scangle_it12.3514.515568
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 630 -
Rwork0.28 11547 -
obs-11547 99.99 %

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