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- PDB-6yj7: DarB fom B. subtilis in complex with AMP -

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Basic information

Entry
Database: PDB / ID: 6yj7
TitleDarB fom B. subtilis in complex with AMP
ComponentsCBS domain-containing protein YkuL
KeywordsUNKNOWN FUNCTION / c-di-AMP binding protein
Function / homology: / : / CBS domain superfamily / ADENOSINE MONOPHOSPHATE / Cyclic di-AMP receptor B
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 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)34,0375
Polymers33,3072
Non-polymers7303
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-40 kcal/mol
Surface area13400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.310, 69.260, 105.420
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-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.26 Å3/Da / Density % sol: 45.67 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris/HCl PH 8.5, 32 % w/v polyethylene glycol 4000, 5 % v/v/ glycerol

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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: P14 (MX2) / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.64→41.94 Å / Num. obs: 37896 / % possible obs: 99.8 % / Redundancy: 13.259 % / Biso Wilson estimate: 37.864 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.028 / Rrim(I) all: 0.029 / Χ2: 1.021 / Net I/σ(I): 40.44 / Num. measured all: 502479 / Scaling rejects: 59
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.64-1.7113.5260.6544.1243160.9740.6899.8
1.71-1.8113.4850.46.5151600.9890.41699.8
1.81-2.0113.3290.17513.675310.9980.18199.9
2.01-813.1970.02365.252051110.024100
8-149.7420.021111.693060.9990.02296.2
14-177.9620.02195.32260.9990.02389.7
17-505.5430.02177.34460.9990.02486.8

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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: 1.64→41.94 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2204 1925 5.1 %
Rwork0.1885 35846 -
obs0.1901 37771 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.79 Å2 / Biso mean: 44.5992 Å2 / Biso min: 20.13 Å2
Refinement stepCycle: final / Resolution: 1.64→41.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2186 0 47 186 2419
Biso mean--36.42 51.55 -
Num. residues----276
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.64-1.680.3251360.27325102646100
1.68-1.730.30061390.23982497263699
1.73-1.780.26911400.22242513265399
1.78-1.830.25561310.214225312662100
1.83-1.90.26431360.208724952631100
1.9-1.980.2331210.206425762697100
1.98-2.070.25321480.204325482696100
2.07-2.170.22781370.197625372674100
2.18-2.310.26161390.193625432682100
2.31-2.490.1911340.20425602694100
2.49-2.740.24661170.214125992716100
2.74-3.140.25271500.210625812731100
3.14-3.950.23341430.17826192762100
3.95-41.940.17021540.15912737289199
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)
11.28250.3020.47821.4422-0.39762.2936-0.06450.0272-0.0487-0.08040.0425-0.04840.2006-0.0173-0.00250.2127-0.00880.03740.2414-0.00730.2923-2.7528-11.033921.2071
21.75590.3470.43651.21390.29382.3971-0.16580.1278-0.0485-0.26290.1496-0.1424-0.16450.3164-0.01040.33610.00670.0950.29430.00430.329510.19143.070511.8341
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A'A3 - 201
2X-RAY DIFFRACTION2chain 'B'B11 - 201

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