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- PDB-3aq1: Open state monomer of a group II chaperonin from methanococcoides... -

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Basic information

Entry
Database: PDB / ID: 3aq1
TitleOpen state monomer of a group II chaperonin from methanococcoides burtonii
ComponentsThermosome subunit
KeywordsCHAPERONE / GROUP II CHAPERONIN / PROTEIN FOLDING
Function / homology
Function and homology information


unfolded protein binding / protein folding / ATP binding
Similarity search - Function
GROEL; domain 2 / TCP-1-like chaperonin intermediate domain / GROEL; domain 1 / GroEL-like equatorial domain / GroEL / GroEL / Thermosome, archaeal / Chaperonins TCP-1 signature 2. / Chaperonin TCP-1, conserved site / Chaperonins TCP-1 signature 3. ...GROEL; domain 2 / TCP-1-like chaperonin intermediate domain / GROEL; domain 1 / GroEL-like equatorial domain / GroEL / GroEL / Thermosome, archaeal / 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 / 3-Layer(bba) Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesMethanococcoides burtonii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.746 Å
AuthorsHarrop, S.J. / Pilak, O. / Siddiqui, K.S. / De Francisci, D. / Burg, D. / Williams, T.J. / Cavicchioli, R. / Curmi, P.M.
CitationJournal: ENVIRON.MICROBIOL. / Year: 2011
Title: Chaperonins from an Antarctic archaeon are predominantly monomeric: crystal structure of an open state monomer.
Authors: Pilak, O. / Harrop, S.J. / Siddiqui, K.S. / Chong, K. / De Francisci, D. / Burg, D. / Williams, T.J. / Cavicchioli, R. / Curmi, P.M.
History
DepositionOct 24, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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

Downloads & links

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Assembly

Deposited unit
B: Thermosome subunit


Theoretical massNumber of molelcules
Total (without water)53,9301
Polymers53,9301
Non-polymers00
Water75742
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thermosome subunit

B: Thermosome subunit


Theoretical massNumber of molelcules
Total (without water)107,8612
Polymers107,8612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+11
Buried area1670 Å2
ΔGint-21 kcal/mol
Surface area37570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.564, 115.256, 193.864
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-540-

HOH

21B-545-

HOH

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Components

#1: Protein Thermosome subunit / / GROUP II CHAPERONIN


Mass: 53930.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcoides burtonii (archaea) / Strain: DSM 6242 / Gene: Mbur_1960 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12UN6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 3.29 Å3/Da / Density % sol: 62.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6M AMSO4, 2.5%(v/v) dioxane, 0.1M Mes/NaOh pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 21, 2008 / Details: osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.73→21.505 Å / Num. all: 18736 / Num. obs: 18736 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 61.3 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 19

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: dev_222)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A6D

1a6d


Resolution: 2.746→21.505 Å / SU ML: 0.42 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.35 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2541 1874 10.01 %RANDOM
Rwork0.1899 ---
all0.1963 18729 --
obs0.1963 18729 98.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.286 Å2 / ksol: 0.315 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.1376 Å2-0 Å20 Å2
2---8.1705 Å2-0 Å2
3---0.033 Å2
Refinement stepCycle: LAST / Resolution: 2.746→21.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3032 0 0 42 3074
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083058
X-RAY DIFFRACTIONf_angle_d1.1054124
X-RAY DIFFRACTIONf_dihedral_angle_d17.2251145
X-RAY DIFFRACTIONf_chiral_restr0.077502
X-RAY DIFFRACTIONf_plane_restr0.003528
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7465-2.84440.31551670.2467150291
2.8444-2.9580.3061860.2249167799
2.958-3.09230.28211860.2077167399
3.0923-3.25480.30951850.2178165799
3.2548-3.45790.31581880.2043169499
3.4579-3.72370.26931880.20271692100
3.7237-4.09610.23151890.17241701100
4.0961-4.68340.21231900.14341710100
4.6834-5.88060.22621930.1551737100
5.8806-21.50560.21122020.18161812100
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)
12.1323-0.95320.47693.2858-0.54611.879-0.0136-0.209-0.1529-0.239-0.06480.1280.0931-0.50040.07770.1237-0.06520.04830.4059-0.06190.160615.998443.165894.6935
22.3106-0.54990.04653.13370.67563.80480.02220.0204-0.1255-0.4288-0.2549-0.56380.24270.0413-0.00320.26220.0063-0.06740.1517-0.11730.333218.40632.192965.0476
32.8127-0.90880.62555.02690.78072.018-0.0235-0.2111-0.0178-0.17370.0335-0.408-0.1878-0.0667-0.01590.35670.0143-0.00020.1733-0.02260.344736.585912.604253.5758
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(RESSEQ 1:96 OR RESSEQ 356:496) AND CHAIN B
2X-RAY DIFFRACTION2(RESSEQ 97:166 OR RESSEQ 320:355) AND CHAIN B
3X-RAY DIFFRACTION3(RESSEQ 167:319) AND CHAIN B

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