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- PDB-6tgs: AtNBR1-PB1 domain -

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Basic information

Entry
Database: PDB / ID: 6tgs
TitleAtNBR1-PB1 domain
ComponentsProtein NBR1 homolog
KeywordsSIGNALING PROTEIN / Autophagy
Function / homology
Function and homology information


vacuole / protein polymerization / ubiquitin binding / autophagy / protein transport / zinc ion binding / cytoplasm
Zinc finger, ZZ-type / PB1 domain / UBA-like superfamily / Immunoglobulin-like fold / Next to BRCA1, central domain / PB1 domain
Protein NBR1 homolog
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsJakobi, A.J. / Sachse, C.
Funding support Germany, 3items
OrganizationGrant numberCountry
European CommissionPIEF-GA-2012-331285 Germany
European CommissionPCOFUND-GA-2008-229597 Germany
German Research FoundationEXC1074 Germany
Validation Report
SummaryFull reportAbout validation report
History
DepositionNov 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein NBR1 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,96511
Polymers10,0531
Non-polymers91210
Water63135
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-13 kcal/mol
Surface area5880 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)43.128, 79.438, 24.135
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-108-

SO4

21A-225-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Protein NBR1 homolog / AtNBR1 / At4g24690


Mass: 10052.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: NBR1, At4g24690, F22K18.110 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9SB64

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Non-polymers , 6 types, 45 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.19 Å3/Da / Density % sol: 43.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES (pH 6.5), 18-20% (w/v) PEG20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.53→37.9 Å / Num. obs: 12367 / % possible obs: 99.2 % / Redundancy: 2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.02799 / Rpim(I) all: 0.02799 / Rsym value: 0.03958 / Net I/σ(I): 10.45
Reflection shellResolution: 1.53→1.585 Å / Rmerge(I) obs: 0.4132 / Mean I/σ(I) obs: 1.42 / Num. unique obs: 1271 / CC1/2: 0.655 / Rpim(I) all: 0.4132 / Rrim(I) all: 0.5844

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Processing

Software
NameVersionClassification
PHENIX(dev_3500: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: EMD-10499

Resolution: 1.53→37.9 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.22 / Phase error: 31
RfactorNum. reflection% reflection
Rfree0.2549 1227 5.16 %
Rwork0.2204 --
Obs0.2221 12367 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.53→37.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms662 0 56 35 753
Refine LS restraints
Refinement-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007783
X-RAY DIFFRACTIONf_angle_d0.91054
X-RAY DIFFRACTIONf_dihedral_angle_d5.793601
X-RAY DIFFRACTIONf_chiral_restr0.057120
X-RAY DIFFRACTIONf_plane_restr0.005138
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefinement-ID% reflection obs (%)
1.53-1.59130.41221040.36682497X-RAY DIFFRACTION97
1.5913-1.66370.38071510.3312501X-RAY DIFFRACTION99
1.6637-1.75140.35761510.31792479X-RAY DIFFRACTION98
1.7514-1.86110.27911270.28442552X-RAY DIFFRACTION99
1.8611-2.00480.24721260.22582541X-RAY DIFFRACTION99
2.0048-2.20660.28331500.21132447X-RAY DIFFRACTION97
2.2066-2.52580.22931570.20492480X-RAY DIFFRACTION99
2.5258-3.18210.2251210.20782536X-RAY DIFFRACTION99
3.1821-39.73240.23291400.19312509X-RAY DIFFRACTION98

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