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- PDB-6yja: DarB fom B. subtilis in complex with c-di-AMP -

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Basic information

Entry
Database: PDB / ID: 6yja
TitleDarB fom B. subtilis in complex with c-di-AMP
ComponentsCBS domain-containing protein YkuL
KeywordsUNKNOWN FUNCTION / c-di-AMP binding protein
Function / homology: / : / CBS domain superfamily / Chem-2BA / Cyclic di-AMP receptor B
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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

Downloads & links

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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)34,7917
Polymers33,3072
Non-polymers1,4845
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-41 kcal/mol
Surface area13560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.150, 65.410, 104.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 231 molecules

#2: Chemical ChemComp-2BA / (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide / bis-(3',5')-cyclic-dimeric-Adenosine-monophosphate


Mass: 658.412 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O12P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.17 Å3/Da / Density % sol: 43.31 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M calcium chloride dehydrate, 0.05 M HEPES sodium pH 7.5, 28 % v/v polyethylene glycol 400, 0.002 M spermine

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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: 1.7→40.91 Å / Num. obs: 32669 / % possible obs: 99.8 % / Redundancy: 7.074 % / Biso Wilson estimate: 32.948 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.052 / Χ2: 0.994 / Net I/σ(I): 24.45 / Num. measured all: 231089 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.767.340.8552.4132310.8860.9299.8
1.76-1.867.0390.5354.2543870.9540.57899.9
1.86-1.966.7580.3028.8135580.980.32799.7
1.96-2.167.2570.1616.4153340.9930.17299.8
2.16-87.0570.03539.99157760.9990.03899.8
8-146.6540.0362.033060.9980.03299.7
14-175.5620.04149.13320.9840.047100
17-504.3560.03843.62450.9960.04393.8

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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: 1.7→40.91 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 24.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2105 1631 5 %
Rwork0.1828 30972 -
obs0.1842 32603 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.43 Å2 / Biso mean: 30.9524 Å2 / Biso min: 13.17 Å2
Refinement stepCycle: final / Resolution: 1.7→40.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2188 0 96 226 2510
Biso mean--24.29 40.79 -
Num. residues----276
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7-1.750.40921330.41825302663
1.75-1.810.44431340.386925322666
1.81-1.870.35681330.296925412674
1.87-1.950.28421350.227225492684
1.95-2.030.22751330.189225412674
2.03-2.140.20211350.171525562691
2.14-2.280.20121350.164325642699
2.28-2.450.23711360.176525882724
2.45-2.70.22391360.181225742710
2.7-3.090.21151370.174826062743
3.09-3.890.17231380.157226362774
3.89-40.910.17141460.164427552901
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)
11.92670.32820.98751.3410.02372.1166-0.0210.0292-0.0228-0.06710.00410.05310.0371-0.07550.00770.15520.01020.01460.13260.00440.1556-3.283-9.873920.6355
22.28870.03880.93931.4788-0.19772.7868-0.04230.0828-0.0401-0.09850.037-0.0819-0.00760.08930.01580.1780.00410.04870.1385-0.00910.189810.12632.698211.6523
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA4 - 199
2X-RAY DIFFRACTION2chain BB10 - 199

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