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- PDB-5d9r: Crystal structure of a conserved domain in the intermembrane spac... -

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Basic information

Entry
Database: PDB / ID: 5d9r
TitleCrystal structure of a conserved domain in the intermembrane space region of the plastid division protein ARC6
ComponentsProtein ACCUMULATION AND REPLICATION OF CHLOROPLASTS 6, chloroplastic
KeywordsBIOSYNTHETIC PROTEIN / plastid division machinery
Function / homology
Function and homology information


response to gibberellin / chloroplast inner membrane / chloroplast organization / chloroplast fission / chloroplast envelope / plastid / chloroplast / : / protein homodimerization activity
Similarity search - Function
ARC6, IMS domain / Protein ACCUMULATION AND REPLICATION OF CHLOROPLASTS 6-like / ARC6-like, IMS domain / Chaperone J-domain superfamily
Similarity search - Domain/homology
Protein ACCUMULATION AND REPLICATION OF CHLOROPLASTS 6, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.052 Å
AuthorsRadhakrishnan, A. / Kumar, N. / Su, C.-C. / Chou, T.-H. / Yu, E.
CitationJournal: Protein Sci. / Year: 2016
Title: Crystal structure of a conserved domain in the intermembrane space region of the plastid division protein ARC6.
Authors: Kumar, N. / Radhakrishnan, A. / Su, C.C. / Osteryoung, K.W. / Yu, E.W.
History
DepositionAug 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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


Theoretical massNumber of molelcules
Total (without water)20,5221
Polymers20,5221
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.339, 60.339, 92.326
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 20522.006 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 BL21 (bacteria) / References: UniProt: Q9FIG9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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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: 2.46 Å3/Da / Density % sol: 47.97 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG4000, magnesium sulfate, tri-sodium citrate, isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 12651 / % possible obs: 99.8 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.037 / Rrim(I) all: 0.087 / Χ2: 1.028 / Net I/av σ(I): 14.159 / Net I/σ(I): 14.2 / Num. measured all: 67102
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.05-2.125.40.39912180.9570.1890.4421.02199.9
2.12-2.215.40.27612590.9720.1310.3061.007100
2.21-2.315.40.2212430.9750.1040.2441.02100
2.31-2.435.40.17512350.9840.0830.1941.059100
2.43-2.585.40.12812400.990.060.1421.017100
2.58-2.785.40.09612630.9950.0450.1061.041100
2.78-3.065.40.08312740.9960.0390.0921.015100
3.06-3.515.30.08212660.9940.0380.0911.044100
3.51-4.425.10.06612960.9960.0310.0731.059100
4.42-504.80.05713570.9960.0270.063198.4

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.15data extraction
SHELXDEphasing
RefinementResolution: 2.052→45.476 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2227 636 5.04 %
Rwork0.2054 --
obs0.2063 12612 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.06 Å2 / Biso mean: 37.8647 Å2 / Biso min: 14.83 Å2
Refinement stepCycle: final / Resolution: 2.052→45.476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1039 0 0 75 1114
Biso mean---44.11 -
Num. residues----132

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