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- PDB-1iok: CRYSTAL STRUCTURE OF CHAPERONIN-60 FROM PARACOCCUS DENITRIFICANS -

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Basic information

Entry
Database: PDB / ID: 1iok
TitleCRYSTAL STRUCTURE OF CHAPERONIN-60 FROM PARACOCCUS DENITRIFICANS
ComponentsCHAPERONIN 60
KeywordsCHAPERONE / chaperonin
Function / homology
Function and homology information


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
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsFukami, T.A. / Yohda, M. / Taguchi, H. / Yoshida, M. / Miki, K.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of chaperonin-60 from Paracoccus denitrificans.
Authors: Fukami, T.A. / Yohda, M. / Taguchi, H. / Yoshida, M. / Miki, K.
#1: Journal: J.CRYST.GROWTH / Year: 1996
Title: Crystallization and Preliminary X-Ray Characterization of Chaperonin-60 from Paracoccus Denitrificans
Authors: Fukami, T.A. / Takasuga, Y. / Sumi, M. / Yohda, M. / Yoshida, M. / Miki, K.
History
DepositionMar 16, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 3, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
A: CHAPERONIN 60
B: CHAPERONIN 60
C: CHAPERONIN 60
D: CHAPERONIN 60
E: CHAPERONIN 60
F: CHAPERONIN 60
G: CHAPERONIN 60


Theoretical massNumber of molelcules
Total (without water)404,5167
Polymers404,5167
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16700 Å2
ΔGint-111 kcal/mol
Surface area147820 Å2
MethodPISA
2
A: CHAPERONIN 60
B: CHAPERONIN 60
C: CHAPERONIN 60
D: CHAPERONIN 60
E: CHAPERONIN 60
F: CHAPERONIN 60
G: CHAPERONIN 60

A: CHAPERONIN 60
B: CHAPERONIN 60
C: CHAPERONIN 60
D: CHAPERONIN 60
E: CHAPERONIN 60
F: CHAPERONIN 60
G: CHAPERONIN 60


Theoretical massNumber of molelcules
Total (without water)809,03214
Polymers809,03214
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area38440 Å2
ΔGint-240 kcal/mol
Surface area290620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)286.355, 286.355, 153.463
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.626133, 0.779704, 0.004449), (-0.779714, 0.626109, 0.005741), (0.001691, -0.007064, 0.999974)-35.9326, 101.26306, 0.37255
2given(-0.215883, 0.976347, 0.011879), (-0.976413, -0.215909, 0.00092), (0.003463, -0.0114, 0.999929)20.59499, 192.73811, 0.73311
3given(-0.900039, 0.435695, 0.00993), (-0.435765, -0.900038, -0.006327), (0.006181, -0.010022, 0.999931)128.63876, 205.54558, 0.38737
4given(-0.901533, -0.432677, 0.005391), (0.432606, -0.901519, -0.010797), (0.009532, -0.007401, 0.999927)205.42465, 129.40227, -0.19825
5given(-0.228419, -0.973561, -0.001897), (0.973502, -0.228382, -0.011628), (0.010887, -0.004503, 0.999931)194.07994, 22.70074, -0.52396
6given(0.6192, -0.785213, -0.005763), (0.785204, 0.619223, -0.004092), (0.006781, -0.001991, 0.999975)102.96165, -35.53516, -0.33774
7given(0.622075, 0.782952, 0.002779), (-0.78295, 0.622051, 0.006503), (0.003363, -0.006221, 0.999975)-35.86661, 102.22952, -0.01005
8given(-0.204779, 0.978807, -0.001244), (-0.978783, -0.204765, 0.007428), (0.007015, 0.002739, 0.999972)19.0661, 191.41692, -1.6097
9given(-0.887431, 0.460712, 0.014524), (-0.460909, -0.887303, -0.016043), (0.005496, -0.020932, 0.999766)123.47654, 207.60902, 1.83574
10given(-0.897571, -0.440857, 0.00331), (0.440809, -0.897547, -0.009809), (0.007296, -0.007345, 0.999946)206.07983, 127.71628, 0.06883
11given(-0.233327, -0.972361, 0.008476), (0.972276, -0.233427, -0.013807), (0.015403, 0.005019, 0.999869)194.3604, 23.63896, -2.39584
12given(0.59287, -0.805202, -0.012447), (0.805281, 0.592888, 0.002576), (0.005305, -0.011551, 0.999919)109.35307, -35.08474, 1.03147
13given(0.623724, 0.781643, 0.001666), (-0.781603, 0.623667, 0.011651), (0.008068, -0.008569, 0.999931)-35.91305, 101.56383, -0.41253
14given(-0.219093, 0.975637, 0.011445), (-0.975626, -0.219209, 0.010065), (0.012328, -0.008961, 0.999884)20.60262, 192.77765, -0.86837
15given(-0.894498, 0.446379, 0.024875), (-0.44661, -0.894718, -0.004399), (0.020293, -0.015044, 0.999681)125.66047, 206.15771, -0.88984
16given(-0.903372, -0.428764, 0.00901), (0.428708, -0.903412, -0.00754), (0.011373, -0.002949, 0.999931)205.04071, 129.94191, -1.11375
17given(-0.220294, -0.975398, 0.00835), (0.975219, -0.220417, -0.019075), (0.020446, 0.003941, 0.999783)192.99123, 21.8897, -2.90347
18given(0.611836, -0.790519, -0.027136), (0.790682, 0.612191, -0.006638), (0.02186, -0.017394, 0.99961)105.92568, -35.21476, -0.60083

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Components

#1: Protein
CHAPERONIN 60 /


Mass: 57787.980 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Paracoccus denitrificans (bacteria) / References: UniProt: Q9Z462

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 13

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Sample preparation

CrystalDensity Matthews: 3.89 Å3/Da / Density % sol: 68.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG 6000, LiCl, Bicine-Na, pH 9.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 9
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
160 mg/mlprotein1drop
24.0 %(w/v)PEG60001reservoir
31.0 M1reservoirLiCl
4100 mMBicine-Na1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONPhoton Factory BL-6B11
SYNCHROTRONPhoton Factory BL-6A21
Detector
TypeIDDetectorDate
FUJI1IMAGE PLATENov 21, 1997
FUJI2IMAGE PLATENov 6, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 582211 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 73.2 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 20.6
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 3.33 / % possible all: 99.3
Reflection
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 50 Å / Num. obs: 103358 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Num. measured all: 582211
Reflection shell
*PLUS
% possible obs: 99.3 % / Redundancy: 5.6 % / Num. unique obs: 10279 / Num. measured obs: 56862 / Mean I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→6 Å / Cross valid method: NULL / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.235 4354 5 %RANDOM
Rwork0.204 ---
obs0.2035 86523 --
all-111973 --
Refinement stepCycle: LAST / Resolution: 3.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25102 0 0 0 25102
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor all: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg0.881

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