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- PDB-5gtb: crystal structure of intermembrane space region of the ARC6-PDV2 ... -

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Basic information

Entry
Database: PDB / ID: 5gtb
Titlecrystal structure of intermembrane space region of the ARC6-PDV2 complex
Components
  • Plastid division protein PDV2
  • Protein ACCUMULATION AND REPLICATION OF CHLOROPLASTS 6, chloroplastic
KeywordsPLANT PROTEIN / beta barrel / key in the lock / complex
Function / homology
Function and homology information


chloroplast fission / chloroplast inner membrane / response to gibberellin / chloroplast outer membrane / chloroplast organization / chloroplast envelope / phosphatidylinositol-4-phosphate binding / plastid / chloroplast / protein homodimerization activity / mitochondrion
Similarity search - Function
Plastid division protein PDV1/PDV2 / ARC6, IMS domain / Protein ACCUMULATION AND REPLICATION OF CHLOROPLASTS 6-like / ARC6-like, IMS domain / Plastid division regulator alpha solenoid domain / Chaperone J-domain superfamily
Similarity search - Domain/homology
Protein ACCUMULATION AND REPLICATION OF CHLOROPLASTS 6, chloroplastic / Plastid division protein PDV2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.871 Å
AuthorsFeng, Y. / Wang, W.
CitationJournal: Nat Plants / Year: 2017
Title: Structural insights into the coordination of plastid division by the ARC6-PDV2 complex
Authors: Wang, W. / Li, J. / Sun, Q. / Yu, X. / Zhang, W. / Jia, N. / An, C. / Li, Y. / Dong, Y. / Han, F. / Chang, N. / Liu, X. / Zhu, Z. / Yu, Y. / Fan, S. / Yang, M. / Luo, S.Z. / Gao, H. / Feng, Y.
History
DepositionAug 19, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Database references
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: Protein ACCUMULATION AND REPLICATION OF CHLOROPLASTS 6, chloroplastic
B: Plastid division protein PDV2


Theoretical massNumber of molelcules
Total (without water)20,0662
Polymers20,0662
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-4 kcal/mol
Surface area8060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.228, 151.228, 100.566
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Protein ACCUMULATION AND REPLICATION OF CHLOROPLASTS 6, chloroplastic


Mass: 17320.494 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ARC6, At5g42480, MDH9.18 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FIG9
#2: Protein/peptide Plastid division protein PDV2 / Protein PLASTID DIVISION2


Mass: 2745.134 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PDV2, At2g16070, F7H1.9 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9XII1

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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: 5.51 Å3/Da / Density % sol: 77.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: PEG2000MME, Tris pH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.871→27.438 Å / Num. obs: 10239 / % possible obs: 93.82 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 33.8
Reflection shellResolution: 2.87→2.92 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HAD

5had


Resolution: 2.871→27.438 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.8
RfactorNum. reflection% reflection
Rfree0.302 460 4.8 %
Rwork0.2651 --
obs0.267 9587 93.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.871→27.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1200 0 0 0 1200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011234
X-RAY DIFFRACTIONf_angle_d1.341675
X-RAY DIFFRACTIONf_dihedral_angle_d16.447446
X-RAY DIFFRACTIONf_chiral_restr0.045197
X-RAY DIFFRACTIONf_plane_restr0.005209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8708-3.28560.3421310.32172608X-RAY DIFFRACTION81
3.2856-4.13730.32281760.27523201X-RAY DIFFRACTION100
4.1373-27.4390.27241530.24073318X-RAY DIFFRACTION100

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