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- PDB-6ekb: Crystal structure of the BSD2 homolog of Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 6ekb
TitleCrystal structure of the BSD2 homolog of Arabidopsis thaliana
ComponentsDnaJ/Hsp40 cysteine-rich domain superfamily protein
KeywordsCHAPERONE / zinc finger / assembly chaperone / Rubisco
Function / homology
Function and homology information


ribulose bisphosphate carboxylase complex assembly / protein folding chaperone complex / chloroplast stroma / chaperone-mediated protein folding / protein folding chaperone / chloroplast / metal ion binding / cytosol
Similarity search - Function
Heat shock protein DnaJ, cysteine-rich domain superfamily
Similarity search - Domain/homology
Protein BUNDLE SHEATH DEFECTIVE 2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsAigner, H. / Wilson, R.H. / Bracher, A. / Calisse, L. / Bhat, J.Y. / Hartl, F.U. / Hayer-Hartl, M.
CitationJournal: Science / Year: 2017
Title: Plant RuBisCo assembly in E. coli with five chloroplast chaperones including BSD2.
Authors: Aigner, H. / Wilson, R.H. / Bracher, A. / Calisse, L. / Bhat, J.Y. / Hartl, F.U. / Hayer-Hartl, M.
History
DepositionSep 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0May 8, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DnaJ/Hsp40 cysteine-rich domain superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5524
Polymers8,3551
Non-polymers1963
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70 Å2
ΔGint-24 kcal/mol
Surface area4330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.708, 55.708, 48.131
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-315-

HOH

21A-325-

HOH

31A-329-

HOH

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Components

#1: Protein DnaJ/Hsp40 cysteine-rich domain superfamily protein / Uncharacterized protein At3g47650 / Uncharacterized protein F1P2.200


Mass: 8355.468 Da / Num. of mol.: 1 / Mutation: K56M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: F1P2.200, At3g47650 / Plasmid: pHUE / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9SN73
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.97 Å3/Da / Density % sol: 58.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20 % PEG 10,000, 8 % ethylene glycol and 0.1 M HEPES-NaOH pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.2826 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2826 Å / Relative weight: 1
ReflectionResolution: 1.91→47.85 Å / Num. obs: 6226 / % possible obs: 99.7 % / Redundancy: 48.6 % / CC1/2: 1 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.02 / Rrim(I) all: 0.14 / Net I/σ(I): 24.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.91-1.9547.44.8523790.7420.6994.90495
8.95-47.8537.60.0468810.0070.04699.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
Aimless0.5.28data scaling
SHELXDEphasing
REFMAC5.8.0155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.1962 / WRfactor Rwork: 0.1763 / FOM work R set: 0.7757 / SU B: 7.811 / SU ML: 0.111 / SU R Cruickshank DPI: 0.1343 / SU Rfree: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2158 277 4.8 %RANDOM
Rwork0.1888 ---
obs0.1901 5503 91.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.81 Å2 / Biso mean: 46.177 Å2 / Biso min: 28.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å2-0 Å2
2---0.44 Å2-0 Å2
3---0.87 Å2
Refinement stepCycle: final / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms432 0 3 29 464
Biso mean--48.76 46.41 -
Num. residues----62
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.019437
X-RAY DIFFRACTIONr_bond_other_d0.0020.02405
X-RAY DIFFRACTIONr_angle_refined_deg1.8141.934583
X-RAY DIFFRACTIONr_angle_other_deg1.0513933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.199561
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.97526.11118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.531570
X-RAY DIFFRACTIONr_dihedral_angle_4_deg0.113151
X-RAY DIFFRACTIONr_chiral_restr0.1120.260
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02531
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02104
LS refinement shellResolution: 1.902→1.951 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.459 20 -
Rwork0.392 314 -
all-334 -
obs--73.57 %
Refinement TLS params.Method: refined / Origin x: 8.4639 Å / Origin y: 22.425 Å / Origin z: 1.0937 Å
111213212223313233
T0.0589 Å20.0216 Å20.0143 Å2-0.0754 Å20.0241 Å2--0.0444 Å2
L2.9729 °23.124 °21.2653 °2-6.705 °21.9861 °2--0.9311 °2
S-0.2147 Å °0.1699 Å °0.1353 Å °-0.4466 Å °0.2182 Å °0.1753 Å °-0.2204 Å °-0.0414 Å °-0.0035 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A68 - 129
2X-RAY DIFFRACTION1B1 - 2

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