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- PDB-9y9y: Crystal structure of DNA integrity scanning protein DisA from Myc... -

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Basic information

Entry
Database: PDB / ID: 9y9y
TitleCrystal structure of DNA integrity scanning protein DisA from Mycobacterium tuberculosis in complex with cyclic di-AMP and bromide
ComponentsDNA integrity scanning protein DisA
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / DisA
Function / homology
Function and homology information


diadenylate cyclase / diadenylate cyclase activity / adenylate cyclase activity / DNA repair / DNA binding / ATP binding
Similarity search - Function
DNA integrity scanning, DisA, linker region / DNA integrity scanning protein, DisA / DisA, linker domain superfamily / DisA bacterial checkpoint controller linker region / : / 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. / RuvA domain 2-like
Similarity search - Domain/homology
Chem-2BA / BROMIDE ION / DNA integrity scanning protein DisA
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.03 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of DNA integrity scanning protein DisA from Mycobacterium tuberculosis in complex with cyclic di-AMP and bromide
Authors: Liu, L. / Lovell, S. / Battaile, K.P.
History
DepositionSep 15, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA integrity scanning protein DisA
B: DNA integrity scanning protein DisA
C: DNA integrity scanning protein DisA
D: DNA integrity scanning protein DisA
E: DNA integrity scanning protein DisA
F: DNA integrity scanning protein DisA
G: DNA integrity scanning protein DisA
H: DNA integrity scanning protein DisA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)318,79123
Polymers315,4128
Non-polymers3,37915
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22180 Å2
ΔGint-68 kcal/mol
Surface area106960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)279.207, 74.640, 197.795
Angle α, β, γ (deg.)90.00, 125.89, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
DNA integrity scanning protein DisA / Cyclic-di-AMP synthase / c-di-AMP synthase / Diadenylate cyclase


Mass: 39426.461 Da / Num. of mol.: 8 / Fragment: T5-S356
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: disA, dacA, Rv3586 / Plasmid: MytuD.17706.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WNW5, diadenylate cyclase
#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.: 4 / Source method: obtained synthetically / Formula: C20H24N10O12P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Br / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.65 Å3/Da / Density % sol: 53.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpheus B12: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Tris/BICINE, pH 8.5, 30 mM NaF, 30 mM NaBr and 30 mM NaI. MytuD.17706.a.B2.PW39404 at 13.1 mg/mL. Screened as ...Details: Morpheus B12: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Tris/BICINE, pH 8.5, 30 mM NaF, 30 mM NaBr and 30 mM NaI. MytuD.17706.a.B2.PW39404 at 13.1 mg/mL. Screened as apo protein but cyclic di-AMP was bound to 4 sites likely acquired from the expression host. Larged ion modeled as a bromide was near each ligand. plate 19967 C12 drop 3, Puck: PSL-1611, Cryo: direct

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Jun 14, 2025
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 3.03→49.1 Å / Num. obs: 64401 / % possible obs: 99.6 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.055 / Rrim(I) all: 0.145 / Χ2: 1.13 / Net I/σ(I): 11.9 / Num. measured all: 442624
Reflection shellResolution: 3.03→3.11 Å / % possible obs: 99.5 % / Redundancy: 7 % / Rmerge(I) obs: 1.572 / Num. measured all: 32945 / Num. unique obs: 4740 / CC1/2: 0.687 / Rpim(I) all: 0.639 / Rrim(I) all: 1.699 / Χ2: 0.99 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(2.0_5806: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.03→48.83 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2681 3213 4.99 %
Rwork0.2298 --
obs0.2317 64366 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.03→48.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19828 0 187 3 20018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00220271
X-RAY DIFFRACTIONf_angle_d0.57527572
X-RAY DIFFRACTIONf_dihedral_angle_d13.4317665
X-RAY DIFFRACTIONf_chiral_restr0.043302
X-RAY DIFFRACTIONf_plane_restr0.0053610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.03-3.080.47021370.38962647X-RAY DIFFRACTION99
3.08-3.120.39451460.36322599X-RAY DIFFRACTION99
3.12-3.170.38181190.33392637X-RAY DIFFRACTION99
3.17-3.230.40621420.32842630X-RAY DIFFRACTION99
3.23-3.290.34521250.33082655X-RAY DIFFRACTION99
3.29-3.350.3631280.32112657X-RAY DIFFRACTION100
3.35-3.420.37631490.3122623X-RAY DIFFRACTION99
3.42-3.490.35341360.2922642X-RAY DIFFRACTION99
3.49-3.570.35551510.28912634X-RAY DIFFRACTION99
3.58-3.660.31161350.26582609X-RAY DIFFRACTION100
3.66-3.760.27421360.25992690X-RAY DIFFRACTION100
3.76-3.870.28911450.24992660X-RAY DIFFRACTION100
3.87-40.31861410.24322640X-RAY DIFFRACTION99
4-4.140.26871470.23962665X-RAY DIFFRACTION100
4.14-4.310.23061330.2042628X-RAY DIFFRACTION100
4.31-4.50.19311410.19172687X-RAY DIFFRACTION99
4.5-4.740.2461390.18392646X-RAY DIFFRACTION100
4.74-5.040.21471410.18782687X-RAY DIFFRACTION100
5.04-5.430.25381500.20552646X-RAY DIFFRACTION99
5.43-5.970.2741680.23342661X-RAY DIFFRACTION99
5.97-6.830.26981300.22752701X-RAY DIFFRACTION99
6.83-8.60.23011310.20172707X-RAY DIFFRACTION100
8.6-48.830.21171430.18182802X-RAY DIFFRACTION99
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.39270.240.94413.3841.30584.1455-0.0815-0.4018-0.34830.34730.0820.02520.1149-0.12670.0310.60220.04230.07630.50030.0620.787117.9489-32.8234-30.6697
21.1293-0.75170.78831.58680.73592.4262-0.0049-0.05420.0898-0.17980.1257-0.0517-0.01650.3166-0.14130.7535-0.0960.03760.7620.13610.805625.8365-23.4986.4998
33.24360.96450.50492.0118-0.26623.09930.2663-0.2356-0.1531-0.19460.03520.1881-0.0383-0.6712-0.30840.8282-0.08490.09261.1260.23730.772217.0853-31.2918.3014
43.7165-0.2759-0.38423.1320.54394.35670.1121-0.6788-0.16570.40060.2609-0.26970.48230.4961-0.33761.07770.0195-0.03491.12450.12991.143832.9633-39.421930.3653
53.17980.6102-0.18884.8518-1.08823.0640.3365-0.16830.10250.9093-0.30610.272-0.36610.1332-0.07950.7437-0.03720.05190.5417-0.08390.695310.67981.466-24.3314
60.92680.21-0.15411.33660.24273.1031-0.00950.07830.0543-0.0092-0.021-0.0331-0.2334-0.22080.04710.6393-0.0432-0.05870.71310.01760.719525.49171.906319.1817
73.3563-0.9131.26065.82150.25576.33090.0474-0.8660.3540.7256-0.08150.35460.74940.44710.21660.72480.1152-0.02910.85650.00410.825840.40987.4818-20.9651
82.609-1.8209-0.78552.2799-0.67224.1796-0.1854-0.35960.52570.24260.197-0.3994-0.3350.4234-0.03330.5746-0.066-0.04210.7237-0.02220.954645.193610.8938-32.0696
91.76160.23133.03662.6940.53195.6808-0.2524-1.47160.0930.7108-0.16730.55661.37910.39230.20431.14450.12810.13781.96610.24540.823752.5804-8.02357.3717
102.16760.62380.90383.5008-1.29011.5109-0.4627-1.5060.35280.36560.2617-0.56760.09161.14260.05490.69680.285-0.0251.7202-0.06180.660253.09470.45233.0323
110.5855-0.02720.54774.1087-0.63570.70990.5642-0.29070.4295-1.1336-0.16250.20690.01610.9305-0.27151.12990.16230.0712.0035-0.38910.922468.24168.56418.3458
120.62230.08780.46131.3752-0.27720.4196-0.2542-0.93480.10810.57770.2863-1.1003-0.5291.00080.07220.760.4007-0.122.294-0.16671.177271.5436-4.26818.4359
133.35860.90840.14160.55161.05223.8186-1.578-0.18420.3877-0.48580.28811.2121-2.65320.05341.10231.26270.1637-0.26861.9481-0.56961.369659.79948.599224.5797
142.9736-1.06740.59550.3787-0.05962.34330.588-0.34830.8797-0.10730.8217-0.1693-0.28810.5881-1.21721.41120.52370.36422.6550.17121.146454.4084.874732.2521
151.74632.64160.37094.04971.43922.47660.64-0.3861-0.41311.3576-0.3575-1.06350.62640.4596-0.29041.10320.0972-0.16440.72740.18110.995351.5392-23.6323-35.5533
162.26240.5090.07392.91620.46013.6481-0.1197-0.3902-0.2685-0.1044-0.1347-0.55020.13281.21010.20360.66880.03320.071.28980.14440.721253.3334-36.0749.0569
173.5263-0.38930.7883.3683-0.22934.01230.48180.58120.8751-0.7477-0.6498-0.4169-0.1619-0.07560.19880.74620.05630.08430.5648-0.02830.721522.377612.4653-57.3921
183.6544-0.29170.41382.0325-1.09583.5782-0.08290.13310.0827-0.1362-0.06080.075-0.08250.08780.13810.66960.0163-0.04510.4424-0.07370.826820.32816.6684-44.014
192.80290.59051.28683.0893-0.53775.11730.20890.4688-0.1884-0.1622-0.1079-0.47340.64250.434-0.09690.53110.00730.03910.5127-0.06770.603615.179.1221-52.5077
200.8069-0.0342-0.37690.1196-0.82541.93480.2230.7979-0.2401-1.0512-0.61840.42660.45850.14960.29421.81140.3098-0.48850.9706-0.21881.22778.03453.9756-87.3963
213.3602-0.9364.13961.54750.86667.8956-0.83210.60250.7435-0.9341-0.05581.3949-1.37720.08180.79661.24710.0585-0.30930.8588-0.03061.254110.49488.6695-78.5627
224.4951-1.8657-3.0384.8693-0.80563.07361.3471-0.82370.372-0.32170.9551-0.08441.32270.8639-1.85121.53460.3672-0.56081.2102-0.15161.67672.199116.6461-87.5165
233.45490.6152-0.74994.4316-0.29665.49831.2479-0.9478-1.06481.271-0.01251.41610.3145-1.1029-1.28811.12930.1244-0.46690.777-0.10991.8555-7.179214.7261-82.0079
240.3732-0.9656-0.15942.81330.96043.3090.48170.8496-1.3305-0.91810.26060.55611.6342-0.7018-0.67851.62660.2465-0.95330.9673-0.09641.9112-4.651115.2355-94.3882
251.7597-0.1607-0.03910.1609-0.34860.87010.2053-0.1182-0.6168-0.075-0.09240.5441.02090.3006-0.59592.01161.0699-2.21441.3748-0.64741.496-0.799425.6047-100.4997
260.7982-0.33310.23862.26220.5081.11160.7726-0.85050.3897-2.05750.19350.26811.3790.6984-0.50832.21760.886-0.74991.7474-0.75411.42456.726925.1993-107.276
272.4134-1.8542-0.17472.8208-0.66115.35530.32621.124-0.0492-0.6974-0.13480.75180.101-0.2781-0.25160.9888-0.04060.02160.6764-0.08690.76084.3061-9.8972-57.0615
282.22050.6871-0.7243.71920.47513.1269-0.07910.12070.0571-0.80640.13030.4452-0.1063-0.1396-0.07010.7873-0.0495-0.02860.6037-0.03270.7362.8769-17.5352-46.9798
291.02080.38992.68551.08080.71145.20960.43720.3783-0.4885-0.0065-0.24990.04840.16430.4746-0.13411.02090.073-0.17161.0806-0.16431.04723.747-22.0268-88.8145
303.4322-0.79460.14841.20160.5423.38760.55780.39330.34-0.0941-0.23061.0088-0.299-0.912-0.45571.04620.1017-0.27341.45170.01331.3705-14.9881-22.0549-106.0685
315.40360.75810.19952.1708-1.4321.2902-0.66662.1452-0.5855-0.70740.48-0.04910.13660.31860.13380.7481-0.12270.24031.0338-0.21970.873434.2609-31.1409-56.8604
322.28540.39062.19862.1396-0.27775.2114-0.3448-0.04290.0138-0.06480.11620.0803-0.81520.76760.28280.9604-0.22970.01071.2982-0.04260.841827.9725-16.7655-102.1915
331.7849-2.1565-0.63694.14411.11733.54980.08040.1390.3061-0.68530.0151-0.3966-0.24880.4585-0.1030.65430.01050.12430.85610.12190.795250.7377-0.9103-55.5235
341.84420.07560.93250.40630.22922.29640.6964-0.80070.55130.0847-0.2223-0.4452-0.1243-0.3987-0.49481.12140.27020.041.3585-0.1661.010834.2573.6032-83.1472
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 143 )
2X-RAY DIFFRACTION2chain 'A' and (resid 144 through 225 )
3X-RAY DIFFRACTION3chain 'A' and (resid 226 through 304 )
4X-RAY DIFFRACTION4chain 'A' and (resid 305 through 354 )
5X-RAY DIFFRACTION5chain 'B' and (resid 5 through 143 )
6X-RAY DIFFRACTION6chain 'B' and (resid 144 through 354 )
7X-RAY DIFFRACTION7chain 'C' and (resid 7 through 32 )
8X-RAY DIFFRACTION8chain 'C' and (resid 33 through 143 )
9X-RAY DIFFRACTION9chain 'C' and (resid 144 through 182 )
10X-RAY DIFFRACTION10chain 'C' and (resid 183 through 239 )
11X-RAY DIFFRACTION11chain 'C' and (resid 240 through 260 )
12X-RAY DIFFRACTION12chain 'C' and (resid 261 through 293 )
13X-RAY DIFFRACTION13chain 'C' and (resid 294 through 337 )
14X-RAY DIFFRACTION14chain 'C' and (resid 338 through 352 )
15X-RAY DIFFRACTION15chain 'D' and (resid 7 through 143 )
16X-RAY DIFFRACTION16chain 'D' and (resid 144 through 354 )
17X-RAY DIFFRACTION17chain 'E' and (resid 6 through 32 )
18X-RAY DIFFRACTION18chain 'E' and (resid 33 through 116 )
19X-RAY DIFFRACTION19chain 'E' and (resid 117 through 143 )
20X-RAY DIFFRACTION20chain 'E' and (resid 144 through 182 )
21X-RAY DIFFRACTION21chain 'E' and (resid 183 through 224 )
22X-RAY DIFFRACTION22chain 'E' and (resid 225 through 239 )
23X-RAY DIFFRACTION23chain 'E' and (resid 240 through 276 )
24X-RAY DIFFRACTION24chain 'E' and (resid 277 through 304 )
25X-RAY DIFFRACTION25chain 'E' and (resid 305 through 322 )
26X-RAY DIFFRACTION26chain 'E' and (resid 323 through 354 )
27X-RAY DIFFRACTION27chain 'F' and (resid 7 through 32 )
28X-RAY DIFFRACTION28chain 'F' and (resid 33 through 143 )
29X-RAY DIFFRACTION29chain 'F' and (resid 144 through 304 )
30X-RAY DIFFRACTION30chain 'F' and (resid 305 through 354 )
31X-RAY DIFFRACTION31chain 'G' and (resid 6 through 143 )
32X-RAY DIFFRACTION32chain 'G' and (resid 144 through 354 )
33X-RAY DIFFRACTION33chain 'H' and (resid 7 through 143 )
34X-RAY DIFFRACTION34chain 'H' and (resid 144 through 229 )

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