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- PDB-5cdi: Chloroplast chaperonin 60b1 of Chlamydomonas -

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Basic information

Entry
Database: PDB / ID: 5cdi
TitleChloroplast chaperonin 60b1 of Chlamydomonas
ComponentsChaperonin 60B1
KeywordsCHAPERONE / CHAPERONIN COMPLEX
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / protein refolding / ATP binding
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 speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.807 Å
AuthorsZhang, S. / Zhou, H. / Yu, F. / Gao, F. / He, J. / Liu, C.
Funding support China, 1items
OrganizationGrant numberCountry
PCCE-2012-TD-01 China
CitationJournal: Bmc Biol. / Year: 2016
Title: Structural insight into the cooperation of chloroplast chaperonin subunits
Authors: Zhang, S. / Zhou, H. / Yu, F. / Bai, C. / Zhao, Q. / He, J. / Liu, C.
History
DepositionJul 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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

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Assembly

Deposited unit
A: Chaperonin 60B1
N: Chaperonin 60B1
B: Chaperonin 60B1
C: Chaperonin 60B1
D: Chaperonin 60B1
E: Chaperonin 60B1
F: Chaperonin 60B1
G: Chaperonin 60B1
H: Chaperonin 60B1
I: Chaperonin 60B1
J: Chaperonin 60B1
K: Chaperonin 60B1
L: Chaperonin 60B1
M: Chaperonin 60B1


Theoretical massNumber of molelcules
Total (without water)828,81214
Polymers828,81214
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area45640 Å2
ΔGint-209 kcal/mol
Surface area343090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.338, 174.390, 213.678
Angle α, β, γ (deg.)90.00, 94.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Chaperonin 60B1


Mass: 59200.883 Da / Num. of mol.: 14 / Fragment: UNP residues 31-580
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CPN60B1, CHLREDRAFT_132530 / Production host: Escherichia coli (E. coli) / References: UniProt: A8JE91
Sequence detailsRESIDUE 138 VAL IS MISSING IN MANY DATABANKS. THE DEPOSITED SEQUENCE CONSISTENT WITH PHYTOZOME ...RESIDUE 138 VAL IS MISSING IN MANY DATABANKS. THE DEPOSITED SEQUENCE CONSISTENT WITH PHYTOZOME DATABANK WITH LOCUS NAME Cre17.g741450.

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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: 3.22 Å3/Da / Density % sol: 61.8 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 10% w/v Polyethylene glycol monomethyl ether 5000, 5% v/v Tacsimate pH 7.0, 0.1 M HEPES pH 7.0
PH range: 7.0 - 8.0

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.807→48.66 Å / Num. all: 101331 / Num. obs: 101331 / % possible obs: 96.7 % / Redundancy: 4 % / Net I/σ(I): 18.27
Reflection shellResolution: 3.8→3.87 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 18.27 / % possible all: 93.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XCK

1xck


Resolution: 3.807→48.657 Å / SU ML: 0.69 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 39.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3254 2002 2.02 %0.5
Rwork0.2749 ---
obs0.276 99304 96.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.807→48.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms55706 0 0 0 55706
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00256043
X-RAY DIFFRACTIONf_angle_d0.59775686
X-RAY DIFFRACTIONf_dihedral_angle_d11.78221266
X-RAY DIFFRACTIONf_chiral_restr0.0229241
X-RAY DIFFRACTIONf_plane_restr0.0029828
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8067-3.90190.40141450.35346471X-RAY DIFFRACTION91
3.9019-4.00730.38081450.33916777X-RAY DIFFRACTION95
4.0073-4.12520.41591320.32766808X-RAY DIFFRACTION95
4.1252-4.25820.37191330.3296919X-RAY DIFFRACTION96
4.2582-4.41030.33091560.30656805X-RAY DIFFRACTION96
4.4103-4.58680.35881290.30866963X-RAY DIFFRACTION97
4.5868-4.79540.36031370.27436924X-RAY DIFFRACTION97
4.7954-5.0480.42731680.31056943X-RAY DIFFRACTION97
5.048-5.36390.3991270.33556952X-RAY DIFFRACTION97
5.3639-5.77740.44251440.33787059X-RAY DIFFRACTION98
5.7774-6.35770.36581420.33617107X-RAY DIFFRACTION99
6.3577-7.2750.35651470.2917216X-RAY DIFFRACTION100
7.275-9.15580.26771510.21877184X-RAY DIFFRACTION100
9.1558-48.66140.23981460.21517174X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 166.997 Å / Origin y: -57.042 Å / Origin z: 55.3497 Å
111213212223313233
T0.2242 Å20.0599 Å2-0.0035 Å2-0.3647 Å20.1688 Å2--0.1496 Å2
L0.0835 °20.0028 °2-0.058 °2-0.5805 °20.1937 °2--0.2417 °2
S-0.0441 Å °-0.0623 Å °0.1462 Å °0.1168 Å °-0.0863 Å °-0.2104 Å °0.0006 Å °0.1228 Å °-0.271 Å °
Refinement TLS groupSelection details: all

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