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- PDB-8waf: Crystal structure of the C-terminal fragment (residues 756-982 wi... -

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Basic information

Entry
Database: PDB / ID: 8waf
TitleCrystal structure of the C-terminal fragment (residues 756-982 with the C864S mutation) 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 / SAD / Resolution: 2.8 Å
AuthorsShimada, A. / Takano, A. / Nakamura, Y. / 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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein CHUP1, chloroplastic


Theoretical massNumber of molelcules
Total (without water)26,4821
Polymers26,4821
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13680 Å2
Unit cell
Length a, b, c (Å)123.340, 123.340, 160.784
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222

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Components

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


Mass: 26482.100 Da / Num. of mol.: 1 / Mutation: C864S
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 6.67 Å3/Da / Density % sol: 81.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 50mM CHES (pH 9.0), 0.2M lithium sulfate, 36% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.97892 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 18407 / % possible obs: 99.9 % / Redundancy: 41.9 % / Rmerge(I) obs: 0.201 / Rpim(I) all: 0.032 / Rrim(I) all: 0.204 / Χ2: 1.032 / Net I/σ(I): 5.5 / Num. measured all: 770816
Reflection shellResolution: 2.8→2.85 Å / Num. unique obs: 882 / CC1/2: 0.836 / Rpim(I) all: 0.512 / Χ2: 1.016 / % possible all: 100

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→44.486 Å / FOM work R set: 0.8123 / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2228 937 5.1 %
Rwork0.2023 17422 -
obs0.2033 18359 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 274.63 Å2 / Biso mean: 71.92 Å2 / Biso min: 37.7 Å2
Refinement stepCycle: final / Resolution: 2.8→44.486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1815 0 0 7 1822
Biso mean---57.49 -
Num. residues----226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091848
X-RAY DIFFRACTIONf_angle_d1.092488
X-RAY DIFFRACTIONf_chiral_restr0.072274
X-RAY DIFFRACTIONf_plane_restr0.004321
X-RAY DIFFRACTIONf_dihedral_angle_d17.048691
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8003-2.94790.30621360.2756239899
2.9479-3.13260.33741420.25962429100
3.1326-3.37440.24241520.23062417100
3.3744-3.71380.24341340.19532469100
3.7138-4.25090.22021230.18212493100
4.2509-5.35420.19191200.18632546100
5.3542-44.4860.20051300.2005267099
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)
11.5525-1.3853-2.26524.11090.42213.77460.03170.0544-0.3976-0.2169-0.0842-0.01740.559-0.19570.1660.4790.03440.04770.5922-0.20620.631527.42835.8823113.546
21.70620.715-0.33825.1156-0.93371.4123-0.03970.3428-0.04690.0966-0.0168-0.0319-0.2231-0.14690.06520.33680.10670.02040.61990.06150.383117.42465.0412123.6196
32.4028-0.58041.00744.5192-1.48932.34140.06220.25490.77920.9919-0.02880.683-1.4786-0.5436-0.10860.92520.23720.08150.5630.15290.802914.425486.652127.0826
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 757 through 829 )A757 - 829
2X-RAY DIFFRACTION2chain 'A' and (resid 830 through 936 )A830 - 936
3X-RAY DIFFRACTION3chain 'A' and (resid 937 through 982 )A937 - 982

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