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- PDB-9wbt: Crystal Structure of Escherichia coli GroEL with Magnesium Ions a... -

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Basic information

Entry
Database: PDB / ID: 9wbt
TitleCrystal Structure of Escherichia coli GroEL with Magnesium Ions and a Phosphorylated Serine Residue-3.2A
Components(Chaperonin GroEL) x 2
KeywordsCHAPERONE / Escherichia coli GroEL
Function / homology
Function and homology information


chaperonin ATPase / isomerase activity / ATP-dependent protein folding chaperone / unfolded protein binding / protein refolding / ATP binding / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / HEXANE-1,6-DIOL / Chaperonin GroEL
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsGuo, Y. / Zhang, L. / Zheng, H. / Li, J. / Han, Q.
Funding support United States, China, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS062836 United States
National Natural Science Foundation of China (NSFC)31860702 China
CitationJournal: To Be Published
Title: Crystal Structure of Escherichia coli GroEL with Magnesium Ions and a Phosphorylated Serine Residue
Authors: Guo, Y. / Zhang, L. / Zheng, H. / Li, J. / Han, Q.
History
DepositionAug 15, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chaperonin GroEL
B: Chaperonin GroEL
C: Chaperonin GroEL
D: Chaperonin GroEL
E: Chaperonin GroEL
F: Chaperonin GroEL
G: Chaperonin GroEL
H: Chaperonin GroEL
I: Chaperonin GroEL
J: Chaperonin GroEL
K: Chaperonin GroEL
L: Chaperonin GroEL
M: Chaperonin GroEL
N: Chaperonin GroEL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)810,15682
Polymers804,04414
Non-polymers6,11268
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area65560 Å2
ΔGint-189 kcal/mol
Surface area288140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.835, 262.165, 284.411
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 14 molecules ABEFHJMCDGIKLN

#1: Protein
Chaperonin GroEL / 60 kDa chaperonin / Chaperonin-60 / Cpn60


Mass: 57471.688 Da / Num. of mol.: 7 / Source method: isolated from a natural source
Details: The sequence of organism Escherichia coli BL21(DE3) is not available during the biocuration, replaced by Q1R3B6 temporarily.
Source: (natural) Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q1R3B6, chaperonin ATPase
#2: Protein
Chaperonin GroEL / 60 kDa chaperonin / Chaperonin-60 / Cpn60


Mass: 57391.711 Da / Num. of mol.: 7 / Source method: isolated from a natural source
Details: GroEL,The sequence of organism Escherichia coli BL21(DE3) is not available during the biocuration, replaced by Q1R3B6 temporarily.
Source: (natural) Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q1R3B6, chaperonin ATPase

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Non-polymers , 5 types, 115 molecules

#3: Chemical...
ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C6H14O2
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical...
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: C2H6OS
#6: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.15 Å3/Da / Density % sol: 60.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Solution contains 3.4 M 1,6-Hexanediol, 0.2 M MgCl2, 2 mM 2-mercaptoethanol, 0.1 M Tris, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 3.2→49.2 Å / Num. obs: 167177 / % possible obs: 99.8 % / Redundancy: 13 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 17.3
Reflection shellResolution: 3.2→3.29 Å / Rmerge(I) obs: 0.71 / Num. unique obs: 16363

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
SCALEPACKdata scaling
HKL-2000data reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→49.2 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.906 / SU B: 20.039 / SU ML: 0.333 / Cross valid method: THROUGHOUT / ESU R Free: 0.454 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2362 8340 5 %RANDOM
Rwork0.19603 ---
obs0.19804 157666 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.063 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0 Å2
2--0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 3.2→49.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms54106 0 364 47 54517
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01254816
X-RAY DIFFRACTIONr_bond_other_d0.0010.01655527
X-RAY DIFFRACTIONr_angle_refined_deg0.8531.82973827
X-RAY DIFFRACTIONr_angle_other_deg0.31.763127950
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.38757334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2.9845308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg7.711010128
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0360.28954
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0263756
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0210540
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.326.82329381
X-RAY DIFFRACTIONr_mcbond_other6.3186.82229378
X-RAY DIFFRACTIONr_mcangle_it9.70412.26536698
X-RAY DIFFRACTIONr_mcangle_other9.70412.26536699
X-RAY DIFFRACTIONr_scbond_it7.5497.62825435
X-RAY DIFFRACTIONr_scbond_other7.5497.62825436
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.7413.75837130
X-RAY DIFFRACTIONr_long_range_B_refined15.86682.84229431
X-RAY DIFFRACTIONr_long_range_B_other15.86682.84229432
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.202→3.285 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 575 -
Rwork0.288 11364 -
obs--97.81 %

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