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- PDB-3kfk: Crystal structures of a group II chaperonin from Methanococcus ma... -

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Basic information

Entry
Database: PDB / ID: 3kfk
TitleCrystal structures of a group II chaperonin from Methanococcus maripaludis
ComponentsChaperonin
KeywordsCHAPERONE / double homo-octameric rings
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / unfolded protein binding / ATP hydrolysis activity / ATP binding / identical protein binding / metal ion binding
Similarity search - Function
Thermosome, archaeal / Chaperonins TCP-1 signature 1. / : / Chaperonins TCP-1 signature 2. / Chaperonin TCP-1, conserved site / Chaperonins TCP-1 signature 3. / Chaperone tailless complex polypeptide 1 (TCP-1) / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily ...Thermosome, archaeal / Chaperonins TCP-1 signature 1. / : / Chaperonins TCP-1 signature 2. / Chaperonin TCP-1, conserved site / Chaperonins TCP-1 signature 3. / Chaperone tailless complex polypeptide 1 (TCP-1) / 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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Chaperonin
Similarity search - Component
Biological speciesMethanococcus maripaludis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.003 Å
AuthorsPereira, J.H. / Ralston, C.Y. / Douglas, N. / Meyer, D. / Knee, K.M. / Goulet, D.R. / King, J.A. / Frydman, J. / Adams, P.D.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Crystal structures of a group II chaperonin reveal the open and closed states associated with the protein folding cycle.
Authors: Pereira, J.H. / Ralston, C.Y. / Douglas, N.R. / Meyer, D. / Knee, K.M. / Goulet, D.R. / King, J.A. / Frydman, J. / Adams, P.D.
History
DepositionOct 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chaperonin
B: Chaperonin
C: Chaperonin
D: Chaperonin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,5508
Polymers222,4574
Non-polymers2,0934
Water00
1
A: Chaperonin
B: Chaperonin
C: Chaperonin
D: Chaperonin
hetero molecules

A: Chaperonin
B: Chaperonin
C: Chaperonin
D: Chaperonin
hetero molecules

A: Chaperonin
B: Chaperonin
C: Chaperonin
D: Chaperonin
hetero molecules

A: Chaperonin
B: Chaperonin
C: Chaperonin
D: Chaperonin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)898,19832
Polymers889,82616
Non-polymers8,37216
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area57240 Å2
ΔGint-268 kcal/mol
Surface area335220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.533, 209.527, 266.862
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 11:240 or resseq 263:519 ) and (not element H) and (not element D)
211chain B and (resseq 11:240 or resseq 263:519 ) and (not element H) and (not element D)
311chain C and (resseq 11:240 or resseq 263:519 ) and (not element H) and (not element D)
411chain D and (resseq 11:240 or resseq 263:519 ) and (not element H) and (not element D)

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Components

#1: Protein
Chaperonin / Chaperonin GroEL (Thermosome / HSP60 family)


Mass: 55614.137 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus maripaludis (archaea) / Gene: hsp60, MMP1515 / Production host: Escherichia coli (E. coli) / References: UniProt: Q877G8
#2: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM

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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: 4.73 Å3/Da / Density % sol: 73.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES buffer pH 6.5, 5 mM spermidine and 30 % of 2-Methyl- 2,4-pentanediol (MPD), VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2008
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 6→58.56 Å / Num. all: 9343 / Num. obs: 9343 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 6→6.21 Å / % possible all: 68.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.4_162)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KFE

3kfe


Resolution: 6.003→58.56 Å / SU ML: 0.85 / σ(F): 1.34 / Phase error: 36.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2704 493 4.77 %
Rwork0.2406 --
obs0.2422 9343 95.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 344.992 Å2 / ksol: 0.289 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--59.3108 Å20 Å2-0 Å2
2--124.455 Å20 Å2
3----65.1442 Å2
Refinement stepCycle: LAST / Resolution: 6.003→58.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14495 0 124 0 14619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.03514724
X-RAY DIFFRACTIONf_angle_d1.4719828
X-RAY DIFFRACTIONf_dihedral_angle_d18.9855712
X-RAY DIFFRACTIONf_chiral_restr0.0622432
X-RAY DIFFRACTIONf_plane_restr0.0112536
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3629X-RAY DIFFRACTIONPOSITIONAL
12B3629X-RAY DIFFRACTIONPOSITIONAL4.004
13C3629X-RAY DIFFRACTIONPOSITIONAL2.737
14D3629X-RAY DIFFRACTIONPOSITIONAL2.238
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
6.0031-6.60650.40241130.35292074X-RAY DIFFRACTION82
6.6065-7.56080.39421180.30252554X-RAY DIFFRACTION100
7.5608-9.51910.25931240.20532575X-RAY DIFFRACTION100
9.5191-58.56550.23141380.22792632X-RAY DIFFRACTION98
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)
14.4433-1.7012-1.17630.5288-2.00846.0909-0.94580.17691.93490.7351.98022.0683-1.43321.114-0.58843.10160.5426-0.12872.17210.43443.5733-29.9181-45.6603-38.4505
24.0827-1.5089-0.07661.42172.28544.6163-1.02043.1005-0.10590.1721-0.20972.43540.2263-2.1466-0.0173.7557-0.07280.03194.90330.26332.6995-24.4422-50.2006-66.4899
34.47872.1007-0.43898.5083-1.5674-0.4994-0.60790.4231-1.31791.32210.8262-0.2496-0.37210.45510.1761.19890.1731-0.28270.8664-0.54591.2431-35.6495-64.3105-17.0191
42.80612.04280.56283.16923.15155.8572-0.7920.69322.73771.4996-0.4701-0.2448-2.23983.40990.20842.2762-0.2810.62821.27490.18752.34620.0974-41.5479-38.6033
50.68531.56670.94763.06062.57492.6188-0.9631.73540.3751-1.7730.52821.2569-0.90351.02870.01482.39180.33630.58764.10470.89192.819719.4005-48.8104-66.3764
69.12870.35630.96595.28363.50423.3521.07680.1066-1.3630.9155-1.12040.6566-0.8096-0.6118-0.08161.5259-0.0742-0.4120.2412-0.23710.97563.4004-50.7637-17.0938
74.6114-6.2454-1.51515.60931.88712.21220.2601-0.5569-0.838-1.531-1.02030.7058-0.84720.47320.3031.8296-0.2706-0.27721.52560.42612.235140.5938-69.1966-17.1226
81.85633.48024.64678.0345.16484.87960.4612-0.2105-0.441.49990.36481.0818.42892.71460.3337-2.998-0.30122.25550.882-0.33031.897758.5659-75.914-38.3263
9-0.15310.0645-0.15972.71540.96360.3176-2.94110.67960.72020.75211.50390.1114-1.8386-1.60170.38635.24860.36810.44843.2442-0.34713.714259.0247-85.4505-66.0196
101.4591-4.3553-0.29954.01942.88832.76450.2067-1.16851.6827-0.1305-0.18410.6082-0.1851.0216-0.25691.0763-0.06640.07271.32450.5642.356853.5528-108.3033-16.8751
117.95414.27292.26641.4550.27766.04350.3746-0.69961.2719-1.0345-0.8907-2.84471.4342-0.680.33561.29950.0250.56741.99060.11813.457262.49-125.6248-38.5754
120.11191.13530.59460.63340.375-0.3569-3.18515.221-0.12233.92640.9013-3.9208-6.27230.7456-4.51477.5708-0.8713-3.85693.63220.11246.867851.169-120.5431-65.4504
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 143:210 or resid 359:398)
2X-RAY DIFFRACTION2chain A and (resid 211:358)
3X-RAY DIFFRACTION3chain A and (resid 1:142 or resid 399:526)
4X-RAY DIFFRACTION4chain B and (resid 143:210 or resid 359:398)
5X-RAY DIFFRACTION5chain B and (resid 211:358)
6X-RAY DIFFRACTION6chain B and (resid 1:142 or resid 399:526)
7X-RAY DIFFRACTION7chain C and (resid 1:142 or resid 399:526)
8X-RAY DIFFRACTION8chain C and (resid 143:210 or resid 359:398)
9X-RAY DIFFRACTION9chain C and (resid 211:358)
10X-RAY DIFFRACTION10chain D and (resid 1:142 or resid 399:526)
11X-RAY DIFFRACTION11chain D and (resid 143:210 or resid 359:398)
12X-RAY DIFFRACTION12chain D and (resid 211:358)

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