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- PDB-8c4j: CdaA-compound 4 complex -

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Basic information

Entry
Database: PDB / ID: 8c4j
TitleCdaA-compound 4 complex
ComponentsDiadenylate cyclase
KeywordsPROTEIN BINDING / Complex
Function / homology
Function and homology information


diadenylate cyclase activity / diadenylate cyclase / cAMP biosynthetic process / adenylate cyclase activity / ATP binding / plasma membrane
Similarity search - Function
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.
Similarity search - Domain/homology
5-methylpyrimidin-4-amine / Diadenylate cyclase
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.83 Å
AuthorsNeumann, P. / Ficner, R.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)SPP1879 Germany
German Research Foundation (DFG)SFB860 Germany
CitationJournal: Microlife / Year: 2023
Title: Computer-aided design of a cyclic di-AMP synthesizing enzyme CdaA inhibitor.
Authors: Neumann, P. / Kloskowski, P. / Ficner, R.
History
DepositionJan 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.country

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0637
Polymers38,7382
Non-polymers3255
Water1,53185
1
A: Diadenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5143
Polymers19,3691
Non-polymers1452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Diadenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5494
Polymers19,3691
Non-polymers1803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.820, 64.550, 129.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 19369.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Not traceable N and C-termini have not been modeled.
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: dacA, cdaA, lmo2120 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Y5E4, diadenylate cyclase
#2: Chemical ChemComp-TI5 / 5-methylpyrimidin-4-amine


Mass: 109.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H7N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.21 Å3/Da / Density % sol: 44.22 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 3.7 M NaCl, 0.1M Na-HEPES pH 8.5 and 3 % DMSO

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Data collection

DiffractionMean temperature: 180 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.8266 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8266 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 31111 / % possible obs: 99.9 % / Redundancy: 8 % / Biso Wilson estimate: 37.55 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.082 / Net I/σ(I): 16.15
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.83-1.933.12245020.773.2461
1.93-2.031.71536520.9011.7821
2.03-2.230.77155330.9820.8021
2.23-80.062169740.9990.0641
8-140.0263540.9990.0281
14-170.0284010.031
17-500.0335610.0351

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.83→38.94 Å / SU ML: 0.2903 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.3228
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2409 1553 5.01 %
Rwork0.2159 29431 -
obs0.2172 30984 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.63 Å2
Refinement stepCycle: LAST / Resolution: 1.83→38.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2347 0 19 85 2451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00782426
X-RAY DIFFRACTIONf_angle_d0.9133279
X-RAY DIFFRACTIONf_chiral_restr0.0648395
X-RAY DIFFRACTIONf_plane_restr0.01418
X-RAY DIFFRACTIONf_dihedral_angle_d12.8496911
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.890.5071390.47392619X-RAY DIFFRACTION99.42
1.89-1.960.42881410.38932654X-RAY DIFFRACTION99.71
1.96-2.030.37351380.33282615X-RAY DIFFRACTION99.71
2.03-2.130.33431390.28792639X-RAY DIFFRACTION99.5
2.13-2.240.31531370.24962621X-RAY DIFFRACTION99.64
2.24-2.380.30011400.24262662X-RAY DIFFRACTION99.75
2.38-2.560.2921410.23232668X-RAY DIFFRACTION99.72
2.56-2.820.2711410.2422666X-RAY DIFFRACTION99.82
2.82-3.230.26891420.23162689X-RAY DIFFRACTION99.86
3.23-4.070.20711450.18382744X-RAY DIFFRACTION99.83
4.07-38.940.18281500.17512854X-RAY DIFFRACTION99.77
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)
12.3017405428-0.04291759127850.3868894029733.461870891180.1438734324662.944292513330.621093386109-0.80837507338-0.4346873567610.819300445661-0.2787410319810.07966946342380.0224077611511-0.278721142996-0.3824703792620.853685826025-0.0564254777159-0.07149013629850.4415339443360.02901576533640.383832791224-21.1366936785-1.18192067587-4.2902803882
22.24779388657-0.818299622721-0.2486568335396.149963895760.6695206881216.57562319642-0.02807625853780.0224765012722-0.0104679272089-0.1833851061430.114366449412-0.0417460808011-0.0843976217848-0.3501920606-0.1128993544650.405224625547-0.0330359962724-0.02077793957940.325558378948-0.01744698887690.36353188112-19.0514419726-1.40802247801-16.8215265124
31.133572525380.2513086373090.8725918559278.636211488960.8673811105712.01903812753-0.26808518741-0.0537079526763-0.0138546913867-0.9053371248740.248894775789-0.813519689899-0.3690380338170.1544477650796.06391349229E-50.437510618946-0.009246909611840.06190163920130.371282190436-0.01376287857710.404802831481-13.21712074024.35065902171-19.565300491
43.779950973562.13843815911.334052193384.37818107496-0.544859774453.61422495031-0.1993414094840.07075381397810.249348803036-0.04729303688560.131624379728-0.146240321944-0.4910200017640.1570574456570.09721127524890.64028065369-0.0167888197592-0.04684399876050.395935149693-0.04773775736860.45429047348-14.276164760311.417612446-14.1054631396
52.30218392788-0.01956378638842.197948925276.38983692895-0.3866069267557.67356084658-0.0742562459519-0.3681829993750.7703890040310.50145565377-0.129670184988-0.376251200697-0.2600769651330.02034876684240.2484430928830.651847746115-0.0084979993184-0.02080787861880.473250732132-0.0324562448120.50005770912-22.82298812379.44340696313-2.83572529249
68.017714181481.301264904291.123429082698.3234521065-0.4941736497357.20209848081-0.0679956115316-0.000978547105481-0.00895302901923-0.4543605793450.117857918170.3950595136710.0680073336462-0.60073854217-0.1086309289290.35564973564-0.01003827820620.008217991450560.306993964589-0.01727030769930.340454081858-16.1698893876-24.0753928589-20.9302760468
70.651425280501-1.43560773768-0.2589739823319.58169116705-1.522245258724.05938494181-0.0467008438102-0.173567433906-0.0001093719115110.7852329625070.140824877064-0.468168782772-0.03675596945670.0187952502277-0.1284121123760.331598672627-0.060145770323-0.0636540240540.35257882075-0.01680661087640.360718526144-13.6061360754-22.1741217005-11.1173214184
83.394638229620.0785111768994-2.315124372916.44500955106-1.068863232025.729004932650.01809267245770.0823717265504-0.189750014782-0.107857800646-0.00101817790924-0.1805447571450.501128474981-0.02187651149-0.04181030110330.399879353232-0.0388052671631-0.05837305883230.334916574928-0.0101714671520.392727100332-11.1587179337-32.5637039132-18.4023341314
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 26 )AA3 - 261 - 24
22chain 'A' and (resid 27 through 63 )AA27 - 6325 - 61
33chain 'A' and (resid 64 through 101 )AA64 - 10162 - 99
44chain 'A' and (resid 102 through 141 )AA102 - 141100 - 139
55chain 'A' and (resid 142 through 155 )AA142 - 155140 - 153
66chain 'B' and (resid 5 through 44 )BC5 - 441 - 42
77chain 'B' and (resid 45 through 101 )BC45 - 10143 - 99
88chain 'B' and (resid 102 through 157 )BC102 - 157100 - 155

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