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- PDB-1fy9: CRYSTAL STRUCTURE OF THE HEXA-SUBSTITUTED MUTANT OF THE MOLECULAR... -

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Basic information

Entry
Database: PDB / ID: 1fy9
TitleCRYSTAL STRUCTURE OF THE HEXA-SUBSTITUTED MUTANT OF THE MOLECULAR CHAPERONIN GROEL APICAL DOMAIN
Components60 KD CHAPERONIN
KeywordsCHAPERONE / Stabilizing mutant
Function / homology
Function and homology information


GroEL-GroES complex / chaperonin ATPase / virion assembly / : / 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 / : / 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 / identical protein binding / membrane / cytosol
Similarity search - Function
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 ...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 / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.2 Å
AuthorsWang, Q. / Buckle, A.M. / Fersht, A.R.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Stabilization of GroEL minichaperones by core and surface mutations.
Authors: Wang, Q. / Buckle, A.M. / Fersht, A.R.
#1: Journal: Protein Sci. / Year: 1999
Title: Design of Highly Stable Functional GroEL Minichaperones
Authors: Wang, Q. / Buckle, A.M. / Foster, N.W. / Johnson, C.M. / Fersht, A.R.
History
DepositionSep 28, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 60 KD CHAPERONIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9462
Polymers20,8541
Non-polymers921
Water99155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.910, 84.520, 35.280
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 60 KD CHAPERONIN


Mass: 20854.031 Da / Num. of mol.: 1 / Fragment: APICAL DOMAIN (RESIDUES 191-376) / Mutation: A212E/A223V/M233L/I305L/E308K/N326T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PRSET A / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6F5
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.71 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.75-0.9M POTASSIUM TARTRATE, 50MM MES SODIUM, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.75-0.90 Msodium potassium tartrate1reservoir
250 mMMES sodium1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.963
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 8, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.963 Å / Relative weight: 1
ReflectionResolution: 2.2→38 Å / Num. all: 11606 / Num. obs: 11590 / % possible obs: 98 % / Observed criterion σ(I): 3 / Redundancy: 11.3 % / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.128 / Net I/σ(I): 7.5
Reflection shellResolution: 2.21→2.33 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.9 / % possible all: 90.6
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 38 Å / Observed criterion σ(I): 3 / Num. measured all: 131065
Reflection shell
*PLUS
% possible obs: 90.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: molecular replacement
Starting model: GROEL(191-376) (PDB ID: 1KID)

1kid


Resolution: 2.2→38 Å / SU B: 8.034 / SU ML: 0.2 / σ(F): 0 / ESU R: 0.32 / ESU R Free: 0.24 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.292 600 5 %RANDOM
Rwork0.257 ---
obs0.265 11590 98 %-
all-11606 --
Displacement parametersBiso mean: 32.9 Å2
Refinement stepCycle: LAST / Resolution: 2.2→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1380 0 6 55 1441
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0060.02
X-RAY DIFFRACTIONp_angle_d0.0240.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0190.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.2693
X-RAY DIFFRACTIONp_mcangle_it2.0145
X-RAY DIFFRACTIONp_scbond_it3.4766
X-RAY DIFFRACTIONp_scangle_it4.7538
X-RAY DIFFRACTIONp_plane_restr0.0162
X-RAY DIFFRACTIONp_chiral_restr0.0870.15
X-RAY DIFFRACTIONp_singtor_nbd0.1840.3
X-RAY DIFFRACTIONp_multtor_nbd0.250.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1640.3
X-RAY DIFFRACTIONp_planar_tor2.23
X-RAY DIFFRACTIONp_staggered_tor16.415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor29.620
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 38 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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