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- PDB-6jzf: Structure of the intermembrane space region of PARC6 -

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Basic information

Entry
Database: PDB / ID: 6jzf
TitleStructure of the intermembrane space region of PARC6
ComponentsPlastid division protein CDP1, chloroplastic
KeywordsPROTEIN BINDING / alpha-beta structure / intermembrane space / division machinery
Function / homology
Function and homology information


plastid inner membrane / plastid fission / chloroplast fission / chloroplast inner membrane / chloroplast organization / chloroplast
Similarity search - Function
ARC6, IMS domain / Protein ACCUMULATION AND REPLICATION OF CHLOROPLASTS 6-like / ARC6-like, IMS domain
Similarity search - Domain/homology
Plastid division protein CDP1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.534 Å
AuthorsFeng, Y. / Liu, Z.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31822012 China
National Natural Science Foundation of China31670766 China
National Natural Science Foundation of China31400635
CitationJournal: To Be Published
Title: Structure of PARC6 from Arabidopsis
Authors: Feng, Y. / Liu, Z.
History
DepositionMay 1, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Plastid division protein CDP1, chloroplastic
B: Plastid division protein CDP1, chloroplastic


Theoretical massNumber of molelcules
Total (without water)40,9202
Polymers40,9202
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-5 kcal/mol
Surface area14320 Å2
Unit cell
Length a, b, c (Å)44.128, 121.669, 130.206
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Plastid division protein CDP1, chloroplastic / ARC6-homolog protein / Protein CHLOROPLAST DIVISION SITE POSITIONING 1 / AtCDP1 / Protein PARALOG OF ARC6


Mass: 20460.119 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CDP1, ARC6H, PARC6, At3g19180, MVI11.9 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8VY16
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
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: 2.14 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: MES, Ammonium sulfate, PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.534→44.45 Å / Num. obs: 14753 / % possible obs: 93.78 % / Redundancy: 10.7 % / CC1/2: 0.992 / Net I/σ(I): 13.2
Reflection shellResolution: 2.534→2.625 Å / Num. unique obs: 760 / CC1/2: 0.811

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
Blu-Icedata collection
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HAD

5had


Resolution: 2.534→44.449 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 27.51
RfactorNum. reflection% reflection
Rfree0.2705 709 4.81 %
Rwork0.2181 --
obs0.2206 14753 93.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.534→44.449 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2447 0 0 13 2460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042495
X-RAY DIFFRACTIONf_angle_d0.8793369
X-RAY DIFFRACTIONf_dihedral_angle_d7.9011507
X-RAY DIFFRACTIONf_chiral_restr0.055373
X-RAY DIFFRACTIONf_plane_restr0.004425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5341-2.72970.2781860.26691651X-RAY DIFFRACTION38
2.7297-3.00440.31621170.25462216X-RAY DIFFRACTION52
3.0044-3.4390.32141410.23752758X-RAY DIFFRACTION64
3.439-4.33220.23721520.20013550X-RAY DIFFRACTION82
4.3322-44.45580.25952130.20783869X-RAY DIFFRACTION91

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