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- PDB-4ki8: Crystal structure of a GroEL-ADP complex in the relaxed allosteri... -

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Basic information

Entry
Database: PDB / ID: 4ki8
TitleCrystal structure of a GroEL-ADP complex in the relaxed allosteric state
ComponentsGroEL proteinGroEL
KeywordsCHAPERONE / Relaxed allosteric state / Asymmetrical / tetradecamer / homoligomer / chaperonin / ATPase / Misfolded protein binding / ATP/ADP binding / GroES binding
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
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
ADENOSINE-5'-DIPHOSPHATE / : / Chaperonin GroEL
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.722 Å
AuthorsFei, X. / Yang, D. / LaRonde-LeBlanc, N. / Lorimer, G.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Crystal structure of a GroEL-ADP complex in the relaxed allosteric state at 2.7 A resolution.
Authors: Fei, X. / Yang, D. / Laronde-Leblanc, N. / Lorimer, G.H.
History
DepositionMay 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Aug 14, 2013Group: Other
Revision 1.3Aug 28, 2013Group: Database references
Revision 1.4Nov 13, 2013Group: Other
Revision 1.5Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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: GroEL protein
B: GroEL protein
C: GroEL protein
D: GroEL protein
E: GroEL protein
F: GroEL protein
G: GroEL protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)407,03060
Polymers400,8317
Non-polymers6,19953
Water10,755597
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32560 Å2
ΔGint-486 kcal/mol
Surface area149700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)235.222, 141.655, 156.693
Angle α, β, γ (deg.)90.00, 113.84, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a tetrdecamer generated from the heptamer in the asymmetric unit by the two fold axis: -x, Y, -Z+(2 0 2).

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Components

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Protein , 1 types, 7 molecules ABCDEFG

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


Mass: 57261.578 Da / Num. of mol.: 7 / Mutation: D83A, R197A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: BN17_41231, ECs5124, groEL, groL, LF82_0923, mopA / Plasmid: pKK233-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q548M1

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Non-polymers , 6 types, 650 molecules

#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 597 / 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: 2.98 Å3/Da / Density % sol: 58.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 34% MPD (v/v), 0.1M acetic acid, 20mM CaCl2, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 26, 2012
RadiationMonochromator: double crystal - liquid nitrogen cooled Si 111
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.72→46.17 Å / Num. all: 125774 / Num. obs: 120240 / % possible obs: 95.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Biso Wilson estimate: 45.2 Å2 / Net I/σ(I): 13.98
Reflection shell
Resolution (Å)Num. unique allDiffraction-ID% possible all
2.72-2.8210710185.3
2.82-2.9311298190.5
2.93-3.0711698193.2
3.07-3.2311936195.4
3.23-3.4312180197
3.43-3.6912315198.1
3.69-4.0712415198.8
4.07-4.6512496199.3
4.65-5.8612548199.4
5.86-46.1712644198.9

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASESphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1xck

1xck


Resolution: 2.722→46.166 Å / SU ML: 0.32 / Isotropic thermal model: isotropic / σ(F): 0.11 / σ(I): 2 / Phase error: 21.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2035 1999 1.66 %random
Rwork0.1655 ---
obs0.1662 120240 95.6 %-
all-125774 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.722→46.166 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26922 0 368 597 27887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01227656
X-RAY DIFFRACTIONf_angle_d0.95537514
X-RAY DIFFRACTIONf_dihedral_angle_d15.1810395
X-RAY DIFFRACTIONf_chiral_restr0.0624526
X-RAY DIFFRACTIONf_plane_restr0.0044827
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.722-2.79010.29471250.23337373X-RAY DIFFRACTION84
2.7901-2.86550.28371330.22287863X-RAY DIFFRACTION89
2.8655-2.94980.24791360.20568059X-RAY DIFFRACTION92
2.9498-3.0450.26241390.19868191X-RAY DIFFRACTION93
3.045-3.15380.21971400.20388351X-RAY DIFFRACTION95
3.1538-3.280.24881430.17978462X-RAY DIFFRACTION96
3.28-3.42930.21011460.16998561X-RAY DIFFRACTION97
3.4293-3.610.19571460.15788663X-RAY DIFFRACTION98
3.61-3.83610.18981470.15498706X-RAY DIFFRACTION99
3.8361-4.13210.18631480.1448720X-RAY DIFFRACTION99
4.1321-4.54760.17361480.13398786X-RAY DIFFRACTION99
4.5476-5.20490.19771490.14788781X-RAY DIFFRACTION99
5.2049-6.55460.21411500.19348843X-RAY DIFFRACTION99
6.5546-46.17270.16191490.14868882X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.4534-0.76040.23882.218-0.08041.0218-0.0208-0.34680.15070.30850.05640.0929-0.16520.0199-0.02270.3109-0.0468-0.02630.323-0.01570.2245343.412336.0243310.3779
23.51040.26530.21612.0239-0.13671.2955-0.0399-0.28750.00930.2050.04150.2382-0.0154-0.1963-0.00240.2513-0.0074-0.01480.2655-0.03070.2705308.558124.9716300.4357
32.45680.57240.70663.4208-0.25291.69720.1064-0.3187-0.09770.2140.03910.3390.146-0.3261-0.13160.2688-0.01710.02330.2887-0.01470.3171294.8537-10.7452295.75
44.1167-2.01521.50174.8985-1.45891.7482-0.06660.07040.0670.3163-0.0136-0.2227-0.0130.05950.08440.2171-0.0206-0.00550.2546-0.06370.3335318.103-36.5071298.4831
53.5999-0.43120.40612.50520.12472.5168-0.1232-0.3713-0.22270.39710.121-0.16570.28430.18250.00670.31190.03430.00380.3130.00790.3742348.4567-49.4007311.0248
63.68510.77810.72523.67570.31381.65110.0599-0.2534-0.32770.2792-0.0171-0.0310.13330.1118-0.0360.24530.0360.01650.33380.03250.339375.7569-23.0733319.3036
72.6782-0.52450.3243.9146-0.01690.7938-0.0088-0.21170.1830.3992-0.01820.0671-0.04060.02790.04660.301-0.0398-0.01010.37510.05640.2058373.810514.727318.9972
85.4055-1.31420.67975.4408-1.48925.68520.0509-1.0806-0.55151.12140.1786-0.3420.3296-0.283-0.09590.9712-0.165-0.03821.090.14030.7112332.558934.5735343.6048
98.11591.68164.35743.59391.29944.01790.4987-1.3255-0.18580.9569-0.3859-0.49950.6578-0.3103-0.25581.0296-0.10030.01351.17360.03610.764297.849724.6975334.4125
105.01-3.3032-0.59779.03753.23933.9033-0.3978-1.33390.59021.64080.6119-0.2901-0.5607-0.0256-0.25651.2932-0.06070.15891.15890.11060.7369278.9647-11.5484328.5766
111.60180.3278-1.30351.1594-1.90184.3784-0.0962-0.9898-0.02680.6779-0.1023-0.3268-0.72920.37040.15180.76610.0072-0.23770.97560.00710.6983299.8657-52.4653325.8796
123.7939-0.1343-0.80553.70380.68111.6656-0.0918-0.51610.67010.3234-0.34050.5612-0.4587-0.4060.45071.05930.1059-0.15040.9977-0.25120.6952333.3414-57.3121342.7347
138.61660.3079-2.75599.1276-2.01187.28580.5939-0.2842-0.32181.3204-0.0032.3632-0.6358-0.4962-0.5431.0519-0.02670.17840.7270.13881.0849367.4202-18.71357.2517
145.95671.0376-1.77144.8218-0.70176.9928-0.2732-0.4325-1.56331.512-0.18470.68771.2737-0.49350.48981.6898-0.00460.46441.0108-0.05591.2051366.097517.5185355.5195
153.3024-1.50030.51183.5076-0.04381.22060.1095-0.19240.33810.1071-0.11810.0911-0.2393-0.02130.02460.3559-0.0745-0.03310.3054-0.03780.3235345.394144.5002306.2132
163.8821-0.38720.58081.97430.46891.6648-0.0115-0.0177-0.03280.0117-0.0030.3287-0.001-0.21750.02240.26970.039-0.01140.2043-0.02120.318303.936230.502294.2784
173.61811.42080.92314.53270.711.40140.0255-0.1673-0.095-0.0930.0820.65720.145-0.2446-0.10590.2563-0.013-0.03290.32550.02570.4181288.4446-11.591288.6606
181.5214-1.4306-0.14586.03570.3731.65970.04810.0931-0.3976-0.351-0.04440.19990.3279-0.1460.00550.2687-0.0535-0.01620.31-0.03580.4507309.8832-50.1806290.1702
194.9341-1.16040.64672.5801-0.60561.5587-0.0514-0.3693-0.28590.23550.0724-0.27340.41670.18650.00120.45330.063-0.00010.29810.02050.4621352.861-57.6292308.8666
201.84120.55150.4372.2344-0.40521.9240.0384-0.3116-0.47630.39040.0224-0.2752-0.08380.1816-0.04380.34840.078-0.0770.4820.03140.5464384.4049-25.247324.7282
211.27230.46730.66036.37050.27631.1706-0.02810.02870.32050.2085-0.0858-0.2964-0.13050.13340.15130.2739-0.0491-0.05420.42620.07160.3084382.534318.8048316.3451
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:179 )A2 - 179
2X-RAY DIFFRACTION2( CHAIN B AND RESID 2:179 )B2 - 179
3X-RAY DIFFRACTION3( CHAIN C AND RESID 2:179 )C2 - 179
4X-RAY DIFFRACTION4( CHAIN D AND RESID 2:108 )D2 - 108
5X-RAY DIFFRACTION5( CHAIN E AND RESID 2:169 )E2 - 169
6X-RAY DIFFRACTION6( CHAIN F AND RESID 2:169 )F2 - 169
7X-RAY DIFFRACTION7( CHAIN G AND RESID 2:179 )G2 - 179
8X-RAY DIFFRACTION8( CHAIN A AND RESID 180:385 )A180 - 385
9X-RAY DIFFRACTION9( CHAIN B AND RESID 180:385 )B180 - 385
10X-RAY DIFFRACTION10( CHAIN C AND RESID 180:386 )C180 - 386
11X-RAY DIFFRACTION11( CHAIN D AND RESID 109:409 )D109 - 409
12X-RAY DIFFRACTION12( CHAIN E AND RESID 170:385 )E170 - 385
13X-RAY DIFFRACTION13( CHAIN F AND RESID 170:355 )F170 - 355
14X-RAY DIFFRACTION14( CHAIN G AND RESID 180:388 )G180 - 388
15X-RAY DIFFRACTION15( CHAIN A AND RESID 386:525 )A386 - 525
16X-RAY DIFFRACTION16( CHAIN B AND RESID 386:525 )B386 - 525
17X-RAY DIFFRACTION17( CHAIN C AND RESID 387:525 )C387 - 525
18X-RAY DIFFRACTION18( CHAIN D AND RESID 410:525 )D410 - 525
19X-RAY DIFFRACTION19( CHAIN E AND RESID 386:525 )E386 - 525
20X-RAY DIFFRACTION20( CHAIN F AND RESID 356:525 )F356 - 525
21X-RAY DIFFRACTION21( CHAIN G AND RESID 389:525 )G389 - 525

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