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- PDB-7d48: apo-form cyclic trinucleotide synthase CdnD -

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Basic information

Entry
Database: PDB / ID: 7d48
Titleapo-form cyclic trinucleotide synthase CdnD
ComponentsCyclic AMP-AMP-GMP synthase
KeywordsTRANSFERASE / cyclic trinucleotide synthesis nucleotidyl transferase
Function / homology
Function and homology information


nucleotide metabolic process / nucleotidyltransferase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / defense response to virus / GTP binding / ATP binding / metal ion binding
Similarity search - Function
Second Messenger Oligonucleotide or Dinucleotide Synthetase domain / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
Cyclic AMP-AMP-GMP synthase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å
AuthorsYang, C.-S. / Hou, M.-H. / Tsai, C.-L. / Wang, Y.-C. / Ko, T.-P. / Chen, Y.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Crystal structure and functional implication of a bacterial cyclic AMP-AMP-GMP synthetase.
Authors: Ko, T.P. / Wang, Y.C. / Tsai, C.L. / Yang, C.S. / Hou, M.H. / Chen, Y.
History
DepositionSep 23, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 19, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Cyclic AMP-AMP-GMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4022
Polymers44,3791
Non-polymers231
Water6,684371
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area16580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.924, 52.924, 344.361
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-649-

HOH

21A-865-

HOH

31A-869-

HOH

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Components

#1: Protein Cyclic AMP-AMP-GMP synthase / cGAS/DncV-like nucleotidyltransferase / CD-NTase


Mass: 44378.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Na is a sodium ion / Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: cdnD02, P853_02262
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0DSP4, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.72 Å3/Da / Density % sol: 54.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 8% v/v Tacsimate, pH 6.0, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.14→30 Å / Num. obs: 27647 / % possible obs: 98.9 % / Redundancy: 8.7 % / Biso Wilson estimate: 27.98 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 17
Reflection shellResolution: 2.14→2.22 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 2.7 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Blu-Icedata collection
HKL-2000data processing
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.15→24.01 Å / SU ML: 0.201 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.513 / Stereochemistry target values: GEOSTD + MONOMER LIBRARY
RfactorNum. reflection% reflection
Rfree0.228 1211 5 %
Rwork0.182 --
obs0.185 24213 86.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.64 Å2
Refinement stepCycle: LAST / Resolution: 2.15→24.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2865 0 1 371 3237
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032952
X-RAY DIFFRACTIONf_angle_d0.5934012
X-RAY DIFFRACTIONf_dihedral_angle_d14.6611774
X-RAY DIFFRACTIONf_chiral_restr0.04427
X-RAY DIFFRACTIONf_plane_restr0.005523
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.240.3062670.2131283X-RAY DIFFRACTION45
2.24-2.340.265880.20111659X-RAY DIFFRACTION58
2.34-2.470.26911250.20262367X-RAY DIFFRACTION83
2.47-2.620.24641500.20452860X-RAY DIFFRACTION99
2.62-2.820.28171530.20382907X-RAY DIFFRACTION100
2.82-3.110.24511550.20342940X-RAY DIFFRACTION100
3.11-3.550.22941540.17892932X-RAY DIFFRACTION100
3.55-4.470.20111560.15742964X-RAY DIFFRACTION99
4.47-24.010.19651630.1713090X-RAY DIFFRACTION96
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)
1-0.2613-0.07020.12090.24370.10330.4584-0.0685-0.14160.11730.1380.05410.0729-0.1384-0.05370.01910.16960.0054-0.00360.2834-0.02150.159945.125145.3316156.7013
20.1708-0.0371-0.05480.28950.26820.7557-0.04360.0857-0.06910.2398-0.0311-0.06140.19050.2608-0.00150.19950.03020.00080.3024-0.04280.213453.742633.8265162.1937
30.04070.01-0.05450.0123-0.02110.0406-0.0558-0.20170.49460.10140.20970.1717-0.2479-0.36610.00410.30660.0147-0.01770.5148-0.14520.484561.429757.4272155.3639
40.8802-0.36340.2780.11590.09420.8488-0.29820.26570.30180.0926-0.0896-0.22830.1440.9419-0.3094-0.04930.07750.04730.397-0.0690.194359.533439.8775148.7749
50.6097-0.06540.21630.466-0.5580.87320.0237-0.05080.0271-0.1089-0.06820.0363-0.04320.1964-0.08690.03320.00450.00780.1525-0.02730.119141.658842.763133.7543
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 76 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 77 THROUGH 154 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 155 THROUGH 174 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 175 THROUGH 223 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 224 THROUGH 355 )

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