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- PDB-8wag: Crystal structure of the C-terminal fragment (residues 716-982) o... -

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Basic information

Entry
Database: PDB / ID: 8wag
TitleCrystal structure of the C-terminal fragment (residues 716-982) of Arabidopsis thaliana CHUP1
ComponentsProtein CHUP1, chloroplastic
KeywordsPLANT PROTEIN / Actin / Actin nucleator / Chloroplast movement / CHLOROPLAST UNUSUAL POSITIONING 1
Function / homologyProtein CHUP1-like / chloroplast relocation / chloroplast outer membrane / chloroplast / cytosol / Protein CHUP1, chloroplastic
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.003 Å
AuthorsShimada, A. / Nakamura, Y. / Takano, A. / Kohda, D.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)KAKENHI 24687014 Japan
Japan Society for the Promotion of Science (JSPS)KAKENHI 25121726 Japan
Japan Society for the Promotion of Science (JSPS)KAKENHI 17K07309 Japan
Japan Society for the Promotion of Science (JSPS)KAKENHI 26119002 Japan
CitationJournal: Plant Cell / Year: 2024
Title: CHLOROPLAST UNUSUAL POSITIONING 1 is a plant-specific actin polymerization factor regulating chloroplast movement.
Authors: Kong, S.G. / Yamazaki, Y. / Shimada, A. / Kijima, S.T. / Hirose, K. / Katoh, K. / Ahn, J. / Song, H.G. / Han, J.W. / Higa, T. / Takano, A. / Nakamura, Y. / Suetsugu, N. / Kohda, D. / Uyeda, T.Q.P. / Wada, M.
History
DepositionSep 7, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein CHUP1, chloroplastic
B: Protein CHUP1, chloroplastic


Theoretical massNumber of molelcules
Total (without water)61,3382
Polymers61,3382
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-27 kcal/mol
Surface area25460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.702, 180.702, 180.702
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 719 - 981 / Label seq-ID: 9 - 271

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein Protein CHUP1, chloroplastic / Protein CHLOROPLAST UNUSUAL POSITIONING 1


Mass: 30668.822 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CHUP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LI74

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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: 4.01 Å3/Da / Density % sol: 69.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM HEPES-NaOH (pH 7.4), 1.1 M sodium malonate, 0.5% (v/v) Jeffamine ED-2001 (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 19727 / % possible obs: 99.9 % / Redundancy: 21.7 % / Biso Wilson estimate: 105.82 Å2 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.03 / Net I/σ(I): 30.6
Reflection shellResolution: 3→3.05 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 973 / CC1/2: 0.693 / Rpim(I) all: 0.501

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6L2X

6l2x
PDB Unreleased entry


Resolution: 3.003→29.314 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.18
RfactorNum. reflection% reflection
Rfree0.2238 1008 5.12 %
Rwork0.1738 --
obs0.1761 19703 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 236.57 Å2 / Biso mean: 94.82 Å2 / Biso min: 42.35 Å2
Refinement stepCycle: final / Resolution: 3.003→29.314 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3791 0 0 0 3791
Num. residues----468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013863
X-RAY DIFFRACTIONf_angle_d1.2885197
X-RAY DIFFRACTIONf_chiral_restr0.051569
X-RAY DIFFRACTIONf_plane_restr0.006667
X-RAY DIFFRACTIONf_dihedral_angle_d18.0341449
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2158X-RAY DIFFRACTION15.282TORSIONAL
12B2158X-RAY DIFFRACTION15.282TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.003-3.16070.3171370.2672642100
3.1607-3.35840.26721450.23542642100
3.3584-3.61730.24471650.19982645100
3.6173-3.98050.21071370.16712651100
3.9805-4.55470.16851540.14612646100
4.5547-5.73140.25421300.17292709100
5.7314-29.3140.21841400.1647276099
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)
12.12430.1613-0.32924.39360.11963.07811.03331.466-0.3123-0.0566-1.06011.12990.3575-0.8394-0.13860.8249-0.1774-0.14820.99730.11131.1083-72.081825.750218.2633
28.89622.97343.59612.40581.11594.39130.11010.8684-0.1833-0.08010.0243-0.39230.43890.4553-0.18340.60340.1315-0.06560.5460.01230.5033-19.653923.570427.7751
32.23230.4718-0.79987.80392.60532.11190.28570.08790.6115-0.71580.02870.2357-0.2529-0.0288-0.29160.46730.13910.01630.57220.07510.747-10.62746.750347.0257
43.58761.1786-0.70374.90991.96476.06720.174-0.22580.9679-0.24910.1584-0.2368-0.55050.2339-0.30040.4893-0.0080.18480.6962-0.31511.1457-7.579266.175259.7147
57.1595-2.1877-0.29397.4213-1.04575.7824-1.0732-0.58831.2021.88150.7882-0.08020.10120.90950.60430.7056-0.07-0.03980.8394-0.06140.8689-11.504959.802369.7841
65.87683.03652.75524.96743.27195.98860.3784-0.3947-1.01140.7531-0.2863-0.03531.0830.1189-0.06160.79480.0542-0.0980.53010.16320.6269-27.569612.473748.6777
73.33261.882-0.43084.09464.29456.9328-0.15560.05270.03180.0704-0.28650.6468-0.80130.31640.08950.71770.0441-0.07480.4530.00340.7247-23.910519.41147.7531
82.0574-1.42871.06112.37550.12361.08440.8116-0.51191.13770.355-0.05060.7981-0.3426-0.3734-0.33240.84490.01140.04360.61990.15210.9881-51.804114.06440.459
97.6375-2.51080.90512.7258-0.52921.13750.3753-0.0964-0.05650.1574-0.05740.85310.1637-0.2341-0.26060.7747-0.05410.02610.4987-0.06771.1164-56.484916.757632.3989
101.12560.53990.34040.28980.10040.2235-0.2676-0.5237-0.4152-0.2091.6822-0.68880.0173-1.1734-1.43941.2464-0.06710.13991.37390.3222.3217-87.950424.119336.2498
113.4703-1.33280.6640.9371-1.47733.58670.22490.3135-0.4132-0.33280.02930.88940.8107-0.0297-0.16650.6576-0.27470.01710.66810.01121.7369-72.351118.372825.5447
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 719 through 765 )A719 - 765
2X-RAY DIFFRACTION2chain 'A' and (resid 766 through 829 )A766 - 829
3X-RAY DIFFRACTION3chain 'A' and (resid 830 through 933 )A830 - 933
4X-RAY DIFFRACTION4chain 'A' and (resid 934 through 981 )A934 - 981
5X-RAY DIFFRACTION5chain 'B' and (resid 719 through 764 )B719 - 764
6X-RAY DIFFRACTION6chain 'B' and (resid 765 through 815 )B765 - 815
7X-RAY DIFFRACTION7chain 'B' and (resid 816 through 829 )B816 - 829
8X-RAY DIFFRACTION8chain 'B' and (resid 830 through 863 )B830 - 863
9X-RAY DIFFRACTION9chain 'B' and (resid 864 through 933 )B864 - 933
10X-RAY DIFFRACTION10chain 'B' and (resid 934 through 947 )B934 - 947
11X-RAY DIFFRACTION11chain 'B' and (resid 948 through 981 )B948 - 981

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