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- PDB-6huw: Crystal structure of CdaA from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 6huw
TitleCrystal structure of CdaA from Bacillus subtilis
ComponentsDiadenylate cyclase
KeywordsTRANSFERASE / c-di-AMP / di-adenylate cyclase
Function / homology
Function and homology information


: / diadenylate cyclase activity / diadenylate cyclase / cAMP biosynthetic process / adenylate cyclase activity / nucleotidyltransferase activity / membrane => GO:0016020 / ATP binding / plasma membrane
Similarity search - Function
YojJ-like (1 / DNA integrity scanning protein, DisA, N-terminal domain / Diadenylate cyclase CdaA, N-terminal domain / CdaA N-terminal transmembrane domain / Diadenylate cyclase CdaA / Diadenylate cyclase / DNA integrity scanning protein, DisA, N-terminal / DNA integrity scanning protein, DisA, N-terminal domain superfamily / DisA bacterial checkpoint controller nucleotide-binding / Diadenylate cyclase (DAC) domain profile. ...YojJ-like (1 / DNA integrity scanning protein, DisA, N-terminal domain / Diadenylate cyclase CdaA, N-terminal domain / CdaA N-terminal transmembrane domain / Diadenylate cyclase CdaA / Diadenylate cyclase / DNA integrity scanning protein, DisA, N-terminal / DNA integrity scanning protein, DisA, N-terminal domain superfamily / DisA bacterial checkpoint controller nucleotide-binding / Diadenylate cyclase (DAC) domain profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Diadenylate cyclase / Cyclic di-AMP synthase CdaA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTosi, T. / Freemont, P.S. / Grundling, A.
CitationJournal: To Be Published
Title: CdaA/GlmM complex in Bacillus subtilis
Authors: Tosi, T. / Hoshiga, F.
History
DepositionOct 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: Diadenylate cyclase
B: Diadenylate cyclase


Theoretical massNumber of molelcules
Total (without water)40,2482
Polymers40,2482
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-10 kcal/mol
Surface area14160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.886, 62.886, 187.324
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Diadenylate cyclase / / DAC / Cyclic-di-AMP synthase / c-di-AMP synthase


Mass: 20123.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria)
Gene: dacA, AX282_00750, B4417_1452, BS21228_13325, C7T97_16060, DJ572_00670, DLD52_20680, SC09_Contig25orf01072
Production host: Escherichia coli (E. coli)
References: UniProt: A0A063XB03, UniProt: Q45589*PLUS, diadenylate cyclase

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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: 2.93 Å3/Da / Density % sol: 57.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium Cacodylate pH 6.5, 0.1M Ammonium Sulfate, 0.3M Sodium Formate, 6% PEG8000, 3% PGA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.8→93.66 Å / Num. obs: 9974 / % possible obs: 100 % / Redundancy: 23.2 % / Biso Wilson estimate: 65.08 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.186 / Net I/σ(I): 18.2
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 24.1 % / Rmerge(I) obs: 1.825 / Mean I/σ(I) obs: 5.9 / Num. unique obs: 1396 / CC1/2: 0.97 / % possible all: 100

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RV7

4rv7


Resolution: 2.8→59.616 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.55
RfactorNum. reflection% reflection
Rfree0.2966 445 4.49 %
Rwork0.2545 --
obs0.2565 9901 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 147.16 Å2 / Biso mean: 69.2376 Å2 / Biso min: 34.35 Å2
Refinement stepCycle: final / Resolution: 2.8→59.616 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2198 0 0 0 2198
Num. residues----290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082230
X-RAY DIFFRACTIONf_angle_d1.1923014
X-RAY DIFFRACTIONf_chiral_restr0.062366
X-RAY DIFFRACTIONf_plane_restr0.007389
X-RAY DIFFRACTIONf_dihedral_angle_d8.3181384
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.8-3.20520.39351490.316530513200
3.2052-4.03810.3331390.292731123251
4.0381-59.62990.25511570.218332933450
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)
13.39860.21740.45765.288-2.86933.50310.6336-0.2685-0.37061.0812-0.4766-0.92570.65840.2083-0.41331.186-0.1433-0.2190.5264-0.03660.588910.974513.309124.4143
21.50730.2732-0.25382.80590.55022.9992-0.0709-0.14190.3078-0.1907-0.1040.11780.3699-0.41630.27560.5878-0.06-0.03810.3518-0.10150.4297-1.668813.335815.763
36.4617-1.46771.88895.2482-1.52563.19950.2660.1336-0.1430.3345-0.5211-0.47660.54860.37450.46790.6626-0.040.01810.278-0.06430.4244.72369.035914.4923
40.1016-0.1453-0.14870.25670.13650.3277-0.51340.53340.5177-2.04720.2444-0.3221-0.18390.09740.14161.1939-0.2217-0.2860.1383-0.04660.95142.553625.89795.897
53.32320.4414-0.04552.8632-0.18081.71140.03850.35930.2295-0.5488-0.11670.1639-0.2499-0.19060.13620.9123-0.0105-0.13960.2569-0.07530.57655.23825.259514.1944
63.76921.7653-3.57045.3641-4.45975.0956-0.3225-1.16940.67660.0345-0.77860.1555-0.97780.5317-1.02351.26070.0709-0.40130.8065-0.31560.51928.481323.181127.8704
74.9272-1.93060.84822.4202-0.16442.19230.30240.4498-0.39130.3995-0.06350.02030.1122-0.1885-0.03340.8335-0.0910.03190.22130.01170.45373.3442-10.579511.6409
87.4418-0.9663-0.69483.53411.84260.95890.21990.14460.43710.6984-0.20740.05760.052-0.3430.37780.802-0.1248-0.06430.1805-0.04630.45284.3051-1.586415.3515
90.4843-0.8057-0.20352.8296-0.93086.31810.6522-0.8010.18060.717-0.56080.0485-0.23870.91350.04840.8748-0.0216-0.14360.35070.07170.49638.117-4.667916.2664
103.4718-1.7037-0.65067.7876-0.94690.3485-0.58960.9418-0.26651.52930.5742-1.7533-0.73851.3512-0.12750.7156-0.0347-0.31561.015-0.13490.903918.6819-17.751718.0075
114.72040.34180.54972.6768-0.54443.60480.1839-0.4728-1.52440.8972-0.372-1.81030.29770.1403-0.20290.91930.0516-0.19560.41080.00950.794112.4088-18.535612.5988
126.0277-4.238-0.32643.8904-0.69584.4878-0.74320.5175-1.5772-0.40750.2110.65950.48040.625-0.4310.9111-0.02060.11510.45170.04010.44753.2167-18.90613.5638
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 107 through 126 )A107 - 126
2X-RAY DIFFRACTION2chain 'A' and (resid 127 through 155 )A127 - 155
3X-RAY DIFFRACTION3chain 'A' and (resid 156 through 183 )A156 - 183
4X-RAY DIFFRACTION4chain 'A' and (resid 184 through 202 )A184 - 202
5X-RAY DIFFRACTION5chain 'A' and (resid 203 through 241 )A203 - 241
6X-RAY DIFFRACTION6chain 'A' and (resid 242 through 252 )A242 - 252
7X-RAY DIFFRACTION7chain 'B' and (resid 107 through 145 )B106 - 145
8X-RAY DIFFRACTION8chain 'B' and (resid 146 through 162 )B146 - 162
9X-RAY DIFFRACTION9chain 'B' and (resid 163 through 183 )B163 - 183
10X-RAY DIFFRACTION10chain 'B' and (resid 184 through 201 )B184 - 201
11X-RAY DIFFRACTION11chain 'B' and (resid 202 through 237 )B202 - 237
12X-RAY DIFFRACTION12chain 'B' and (resid 238 through 252 )B238 - 252

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