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- PDB-6jd6: An ankyrin-repeat protein complex guides cargos from inner envelo... -

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Basic information

Entry
Database: PDB / ID: 6jd6
TitleAn ankyrin-repeat protein complex guides cargos from inner envelope to thylakoid Tat pathway
Components
  • Ankyrin repeat domain-containing protein EMB506, chloroplastic
  • Ankyrin repeat domain-containing protein, chloroplastic
KeywordsTRANSPORT PROTEIN / ankyrin-repea / envelope / thylakoid
Function / homology
Function and homology information


chloroplast / molecular condensate scaffold activity
Similarity search - Function
Ankyrin repeats (many copies) / Ankyrin repeat-containing domain / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ankyrin repeat-containing domain superfamily ...Ankyrin repeats (many copies) / Ankyrin repeat-containing domain / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ankyrin repeat-containing domain superfamily / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Ankyrin repeat domain-containing protein, chloroplastic / Ankyrin repeat domain-containing protein EMB506, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsOuyang, M. / Zhang, L.X.
CitationJournal: To Be Published
Title: An ankyrin-repeat protein complex guides cargos from inner envelope to thylakoid Tat pathway
Authors: Ouyang, M. / Zhang, L.X.
History
DepositionJan 31, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ankyrin repeat domain-containing protein EMB506, chloroplastic
B: Ankyrin repeat domain-containing protein, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,15312
Polymers76,1922
Non-polymers96110
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8690 Å2
ΔGint-177 kcal/mol
Surface area16540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)216.816, 216.816, 216.816
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number214
Space group name H-MI4132
Components on special symmetry positions
IDModelComponents
11B-456-

HOH

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Components

#1: Protein Ankyrin repeat domain-containing protein EMB506, chloroplastic / Protein EMBRYO DEFECTIVE 506


Mass: 31227.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: EMB506, At5g40160, MSN9.60 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SQK3
#2: Protein Ankyrin repeat domain-containing protein, chloroplastic / AKRP / Protein EMBRYO DEFECTIVE 2036


Mass: 44964.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AKRP, AKR, EMB2036, At5g66055, K2A18.13 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05753
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.79 Å3/Da / Density % sol: 55.87 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 100mM Hepes pH 7.0, 0.2mM (NH4)2SO4, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 44172 / % possible obs: 100 % / Redundancy: 9.8 % / Biso Wilson estimate: 40.74 Å2 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.026 / Rrim(I) all: 0.08 / Χ2: 0.544 / Net I/σ(I): 5.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.2-2.249.721640.7550.3540.444100
2.24-2.289.821770.7750.3020.6381000.9050.956
2.28-2.329.421700.8510.2310.4441000.6770.716
2.32-2.371021780.9070.1990.4371000.6060.638
2.37-2.4210.221720.9240.1720.4491000.5260.554
2.42-2.4810.121890.9430.1490.441000.4540.479
2.48-2.549.921930.9630.120.4541000.3630.383
2.54-2.619.721760.9690.1010.4531000.3020.319
2.61-2.699.322010.980.0850.5051000.2470.262
2.69-2.779.921510.9860.0660.471000.20.211
2.77-2.879.421980.9910.0550.4731000.1610.171
2.87-2.9910.222070.9930.0450.4891000.1370.145
2.99-3.1210.121810.9950.0380.4941000.1160.122
3.12-3.291022140.9970.0280.5251000.0860.091
3.29-3.499.422140.9980.0240.6351000.070.074
3.49-3.769.722270.9980.0190.7241000.0580.061
3.76-4.1410.122260.9990.0150.7711000.0470.05
4.14-4.749.822490.9990.0130.7599.90.040.042
4.74-5.979.322820.9990.0130.661000.0380.04
5.97-509.224030.9990.010.61399.50.0310.032

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.2 Å48.48 Å
Translation3.2 Å48.48 Å

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASER2.3.0phasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4hb5

4hb5


Resolution: 2.2→48.482 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.62
RfactorNum. reflection% reflection
Rfree0.1865 2221 5.04 %
Rwork0.166 --
obs0.167 44071 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 136.24 Å2 / Biso mean: 46.5 Å2 / Biso min: 25.19 Å2
Refinement stepCycle: final / Resolution: 2.2→48.482 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3089 0 50 292 3431
Biso mean--97.08 56.16 -
Num. residues----391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043185
X-RAY DIFFRACTIONf_angle_d0.8114317
X-RAY DIFFRACTIONf_chiral_restr0.058501
X-RAY DIFFRACTIONf_plane_restr0.004543
X-RAY DIFFRACTIONf_dihedral_angle_d13.3181200
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2003-2.24810.25591550.236725762731
2.2481-2.30040.22071310.226225682699
2.3004-2.3580.22831310.196725862717
2.358-2.42170.19651320.19325802712
2.4217-2.4930.20231280.180625952723
2.493-2.57340.21781230.176525802703
2.5734-2.66540.1821160.169926132729
2.6654-2.77210.18291310.16725962727
2.7721-2.89830.20241380.171326082746
2.8983-3.0510.20851440.180625972741
3.051-3.24220.2181460.178625942740
3.2422-3.49240.18411470.15526112758
3.4924-3.84380.16721530.15226222775
3.8438-4.39960.16741530.137126322785
4.3996-5.54180.14671370.152726822819
5.5418-48.49330.20171560.174328102966
Refinement TLS params.Method: refined / Origin x: -11.3632 Å / Origin y: 28.5078 Å / Origin z: 13.8626 Å
111213212223313233
T0.2995 Å20.0886 Å2-0.0452 Å2-0.2182 Å2-0.0235 Å2--0.2614 Å2
L1.1509 °2-0.5959 °20.6233 °2-2.351 °2-1.3141 °2--2.1233 °2
S0.0496 Å °0.0138 Å °-0.1149 Å °0.0221 Å °0.0485 Å °0.0781 Å °0.0409 Å °-0.0571 Å °-0.0841 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA32 - 230
2X-RAY DIFFRACTION1allB59 - 250
3X-RAY DIFFRACTION1allC1 - 10
4X-RAY DIFFRACTION1allS1 - 407

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