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- PDB-5u9l: Crystal structure of the intermembrane space region of the plasti... -

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Basic information

Entry
Database: PDB / ID: 5u9l
TitleCrystal structure of the intermembrane space region of the plastid division protein PARC6
ComponentsPARALOG OF ACCUMULATION AND REPLICATION OF CHLOROPLASTS 6 (PARC6)
KeywordsCELL CYCLE / Plastid / cell division / chloroplast / intermembrane space
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 / Plastid division regulator alpha solenoid domain
Similarity search - Domain/homology
Plastid division protein CDP1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.516 Å
AuthorsDelmar, J.D. / Chou, T.H.
CitationJournal: To Be Published
Title: Cocrystal structure of the intermembrane space region of the plastid division proteins PARC6 and PDV1
Authors: Delmar, J.A. / Yu, E.W. / Osteryoung, K.W.
History
DepositionDec 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PARALOG OF ACCUMULATION AND REPLICATION OF CHLOROPLASTS 6 (PARC6)
B: PARALOG OF ACCUMULATION AND REPLICATION OF CHLOROPLASTS 6 (PARC6)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1164
Polymers53,0682
Non-polymers492
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-26 kcal/mol
Surface area14700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.533, 124.546, 130.046
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-1005-

HOH

21B-1022-

HOH

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Components

#1: Protein PARALOG OF ACCUMULATION AND REPLICATION OF CHLOROPLASTS 6 (PARC6) / ARC6-homolog protein / Protein CHLOROPLAST DIVISION SITE POSITIONING 1 / AtCDP1 / Protein PARALOG OF ARC6


Mass: 26533.930 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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 1.7 Å3/Da / Density % sol: 27.6 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 18% polyethylene glycol (PEG) 4000, 0.1 M Magnesium acetate, 0.1 M Na-MES (pH 6.5), 0.05 M Potassium nitrate and 5% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 12543 / % possible obs: 99.5 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 6.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.5-2.670.9070.658198.4
2.6-2.728.10.6690.801199.6
2.72-2.868.10.4550.907199.9
2.86-3.0480.3370.939199.9
3.04-3.288.10.2420.966199.1
3.28-3.618.90.1760.984199.9
3.61-4.138.40.1410.986199.4
4.13-5.29.30.1060.9931100
5.2-408.90.0950.996199.1

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
Cootmodel building
MOLREPphasing
RefinementResolution: 2.516→39.91 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28
RfactorNum. reflection% reflection
Rfree0.2594 619 4.94 %
Rwork0.1812 --
obs0.1851 12520 98.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 165.26 Å2 / Biso mean: 65.9137 Å2 / Biso min: 27.85 Å2
Refinement stepCycle: final / Resolution: 2.516→39.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2459 0 2 53 2514
Biso mean--61.95 69.49 -
Num. residues----303
Refinement TLS params.Method: refined / Origin x: -8.7325 Å / Origin y: -17.6226 Å / Origin z: -0.9824 Å
111213212223313233
T0.2945 Å2-0.0093 Å20.023 Å2-0.3148 Å2-0.028 Å2--0.3436 Å2
L0.9696 °2-0.5101 °20.8402 °2-1.5276 °2-1.0414 °2--2.1999 °2
S-0.0934 Å °0.0284 Å °-0.0874 Å °0.0558 Å °0.0609 Å °-0.0222 Å °-0.105 Å °0.0003 Å °-0.0006 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA641 - 818
2X-RAY DIFFRACTION1allB642 - 817
3X-RAY DIFFRACTION1allS1 - 54
4X-RAY DIFFRACTION1allD1 - 2

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