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- PDB-5x9v: Crystal structure of group III chaperonin in the Closed state -

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Basic information

Entry
Database: PDB / ID: 5x9v
TitleCrystal structure of group III chaperonin in the Closed state
ComponentsThermosome, alpha subunit
KeywordsCHAPERONE / group III / Archaeal-like bacterial chaperonin / closed states / pivot joints / ancestral CPN60
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / unfolded protein binding / ATP hydrolysis activity / ATP binding / metal ion binding / identical protein binding / cytoplasm
Similarity search - Function
GROEL; domain 1 / GroEL-like equatorial domain / 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 ...GROEL; domain 1 / GroEL-like equatorial domain / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Thermosome, alpha subunit
Similarity search - Component
Biological speciesCarboxydothermus hydrogenoformans Z-2901 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.003 Å
AuthorsAn, Y.J. / Cha, S.S.
CitationJournal: Nat Commun / Year: 2017
Title: Structural and mechanistic characterization of an archaeal-like chaperonin from a thermophilic bacterium
Authors: An, Y.J. / Rowland, S.E. / Na, J.H. / Spigolon, D. / Hong, S.K. / Yoon, Y.J. / Lee, J.H. / Robb, F.T. / Cha, S.S.
History
DepositionMar 9, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thermosome, alpha subunit
B: Thermosome, alpha subunit
C: Thermosome, alpha subunit
D: Thermosome, alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,88212
Polymers226,7604
Non-polymers2,1228
Water00
1
A: Thermosome, alpha subunit
B: Thermosome, alpha subunit
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)915,52848
Polymers907,04016
Non-polymers8,48832
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_656-x+1,y,-z+11
crystal symmetry operation6_566x,-y+1,-z+11
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area87280 Å2
ΔGint-512 kcal/mol
Surface area278910 Å2
MethodPISA
2
C: Thermosome, alpha subunit
D: Thermosome, alpha subunit
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)915,52848
Polymers907,04016
Non-polymers8,48832
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area87800 Å2
ΔGint-518 kcal/mol
Surface area278910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.166, 186.166, 160.742
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number89
Space group name H-MP422

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Components

#1: Protein
Thermosome, alpha subunit / chaperonin


Mass: 56689.996 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carboxydothermus hydrogenoformans Z-2901 (bacteria)
Strain: Z-2901 / Gene: CHY_0413 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3AF10
#2: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg

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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: 3.07 Å3/Da / Density % sol: 59.95 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 7.5
Details: 3 mM AMP-PNP, 20 mM MgCl2, 100 mM HEPES NaOH (pH 7.5), 22% Polyacrylic Acid 5100

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 56297 / % possible obs: 99.1 % / Redundancy: 14.9 % / Net I/σ(I): 24.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
HKL-2000data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KFE

3kfe


Resolution: 3.003→45.152 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.51 / Phase error: 24.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2582 2000 3.55 %
Rwork0.1985 --
obs0.2007 56286 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.003→45.152 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14652 0 128 0 14780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01514956
X-RAY DIFFRACTIONf_angle_d1.2220268
X-RAY DIFFRACTIONf_dihedral_angle_d15.3775448
X-RAY DIFFRACTIONf_chiral_restr0.0622440
X-RAY DIFFRACTIONf_plane_restr0.0052600
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0027-3.07770.39421380.3043761X-RAY DIFFRACTION98
3.0777-3.16090.31141410.28523794X-RAY DIFFRACTION99
3.1609-3.25390.3231400.26333841X-RAY DIFFRACTION99
3.2539-3.35890.31451400.24533788X-RAY DIFFRACTION98
3.3589-3.47890.33161410.24293813X-RAY DIFFRACTION99
3.4789-3.61820.34031400.2383812X-RAY DIFFRACTION98
3.6182-3.78270.33651420.22983844X-RAY DIFFRACTION99
3.7827-3.98210.26431420.19333852X-RAY DIFFRACTION99
3.9821-4.23140.22331420.17493873X-RAY DIFFRACTION99
4.2314-4.55780.21811440.16213887X-RAY DIFFRACTION99
4.5578-5.01590.19161440.15543919X-RAY DIFFRACTION100
5.0159-5.74050.22041440.18333939X-RAY DIFFRACTION100
5.7405-7.22760.23861480.18463997X-RAY DIFFRACTION100
7.2276-45.1570.1951540.1454166X-RAY DIFFRACTION99

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