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- PDB-6yj8: DarB-APO -

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Basic information

Entry
Database: PDB / ID: 6yj8
TitleDarB-APO
ComponentsCBS domain-containing protein YkuL
KeywordsUNKNOWN FUNCTION / c-di-AMP binding protein
Function / homology: / : / CBS domain superfamily / ACETATE ION / DI(HYDROXYETHYL)ETHER / Cyclic di-AMP receptor B
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsHeidemann, J.L. / Neumann, P. / Ficner, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: To Be Published
Title: DarB from B. subtilis
Authors: Heidemann, J.L. / Neumann, P. / Ficner, R.
History
DepositionApr 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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: CBS domain-containing protein YkuL
B: CBS domain-containing protein YkuL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4724
Polymers33,3072
Non-polymers1652
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-25 kcal/mol
Surface area13400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.670, 67.760, 103.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CBS domain-containing protein YkuL


Mass: 16653.346 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Gene: ykuL, BSU14130 / Production host: Escherichia coli (E. coli) / References: UniProt: O31698
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.04 Å3/Da / Density % sol: 39.84 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M calcium acetate, 0.1 M MES pH 6.5, 15 % w/v polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.84→41.24 Å / Num. obs: 24397 / % possible obs: 99.1 % / Redundancy: 5.187 % / Biso Wilson estimate: 37.219 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.058 / Χ2: 1 / Net I/σ(I): 16.81 / Num. measured all: 126541
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.84-1.885.3110.5772.5117820.8730.6499.7
1.88-1.945.2020.4483.2717640.9110.49999.7
1.94-2.044.8570.34.7228710.9550.33899.8
2.04-2.245.2910.1619.0543420.9810.1899.7
2.24-85.2210.04425.12133070.9980.04998.8
8-144.6230.03439.212650.9990.03893
14-174.9030.0441.06310.9990.04591.2
17-503.9140.04532.09350.9950.05277.8

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YAV

1yav


Resolution: 1.84→41.24 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 26.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2509 1219 5 %
Rwork0.2023 23141 -
obs0.2047 24360 99.16 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.83 Å2 / Biso mean: 36.6232 Å2 / Biso min: 17.25 Å2
Refinement stepCycle: final / Resolution: 1.84→41.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2177 0 11 175 2363
Biso mean--59.79 43.04 -
Num. residues----275
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.84-1.910.41891330.357425242657100
1.91-20.3131350.299625522687100
2-2.10.28541330.242225292662100
2.1-2.230.24221350.214925612696100
2.23-2.410.25731340.21072562269699
2.41-2.650.25121350.208625592694100
2.65-3.030.27361360.21725892725100
3.03-3.820.24331370.19332604274199
3.82-41.240.21861410.16622661280296
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.71810.54221.3751.21950.16331.5806-0.10810.0746-0.004-0.18910.04880.0371-0.04790.08830.03620.2414-0.02910.03090.2060.00230.2161-3.2872-11.074420.682
21.7450.01360.89131.4627-0.16032.9017-0.04770.1808-0.0402-0.14140.019-0.0908-0.02970.0420.02610.1709-0.00120.06520.1642-0.00740.188310.17912.636511.1088
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA3 - 144
2X-RAY DIFFRACTION2chain BB10 - 142

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