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- PDB-7d4j: ddATP complex of cyclic trinucleotide synthase CdnD -

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Basic information

Entry
Database: PDB / ID: 7d4j
TitleddATP complex of cyclic trinucleotide synthase CdnD
ComponentsCyclic AMP-AMP-GMP synthase
KeywordsTRANSFERASE / substrate analogue dideoxy adenosine triphosphate 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
2',3'-dideoxyadenosine triphosphate / Cyclic AMP-AMP-GMP synthase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 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 24, 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 1.3Nov 29, 2023Group: 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: Cyclic AMP-AMP-GMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9024
Polymers44,3791
Non-polymers5243
Water6,720373
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-7 kcal/mol
Surface area16060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.173, 53.173, 345.758
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-762-

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
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-DDS / 2',3'-dideoxyadenosine triphosphate


Mass: 475.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H16N5O11P3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / 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: 2.75 Å3/Da / Density % sol: 55.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 2 mM ddATP, 10 mM GTP, 10 mM MgCl2, 0.2 M ammonium tartrate dibasic, pH 7.0, 26% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 0.9998 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 30653 / % possible obs: 99.1 % / Redundancy: 9.7 % / Biso Wilson estimate: 24.14 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 25
Reflection shellResolution: 2.09→2.16 Å / Redundancy: 5 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 3.4 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Blu-Icedata collection
HKL-2000data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 7D48

7d48


Resolution: 2.09→28.37 Å / SU ML: 0.195 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.305 / Stereochemistry target values: GEOSTD + MONOMER LIBRARY
RfactorNum. reflection% reflection
Rfree0.21 1446 5 %
Rwork0.176 --
obs0.178 28906 93.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.84 Å2
Refinement stepCycle: LAST / Resolution: 2.09→28.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2793 0 31 373 3197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042897
X-RAY DIFFRACTIONf_angle_d0.753941
X-RAY DIFFRACTIONf_dihedral_angle_d17.7641731
X-RAY DIFFRACTIONf_chiral_restr0.044417
X-RAY DIFFRACTIONf_plane_restr0.005506
LS refinement shellResolution: 2.09→2.17 Å
RfactorNum. reflection% reflection
Rfree0.2418 86 -
Rwork0.2087 1636 -
obs--58 %
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)
10.04820.07180.10650.41190.24711.1615-0.0773-0.03160.05210.1499-0.0140.00480.09620.1616-0.15340.09670.02590.0360.1284-0.01660.074146.878338.5997160.2853
20.5777-0.1854-0.04930.2882-0.08270.6401-0.21250.00330.14610.1410.0136-0.2271-0.24040.446-0.16930.02490.02180.00990.252-0.00950.197559.965642.5893152.8052
30.6159-0.02140.46040.6933-0.39150.95610.05440.05690.0397-0.1618-0.10120.03460.03820.1263-0.14160.0540.01340.01220.0574-0.0240.058541.29842.8296134.3581
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 130 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 131 THROUGH 223 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 224 THROUGH 355 )

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