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- PDB-7d4u: ATP complex with double mutant cyclic trinucleotide synthase CdnD -

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Basic information

Entry
Database: PDB / ID: 7d4u
TitleATP complex with double mutant cyclic trinucleotide synthase CdnD
ComponentsCyclic AMP-AMP-GMP synthase
KeywordsTRANSFERASE / cyclic trinucleotide synthesis nucleotidyl transferase substrate complex active-site double mutant
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
ADENOSINE-5'-TRIPHOSPHATE / Cyclic AMP-AMP-GMP synthase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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

Downloads & links

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Assembly

Deposited unit
A: Cyclic AMP-AMP-GMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4213
Polymers44,4071
Non-polymers1,0142
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint-2 kcal/mol
Surface area15180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.864, 118.221, 102.381
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-617-

HOH

21A-624-

HOH

31A-639-

HOH

41A-664-

HOH

51A-672-

HOH

61A-687-

HOH

71A-696-

HOH

81A-697-

HOH

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Components

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


Mass: 44406.824 Da / Num. of mol.: 1 / Mutation: D69K,D71K
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-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.35 Å3/Da / Density % sol: 47.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 5 mM ATP, 10 mM GTP, 10 mM MgCl2, 5% w/v 1-butyl-3-methylimidazolium chloride, pH 7.4, 20% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 11739 / % possible obs: 99.7 % / Redundancy: 6.9 % / Biso Wilson estimate: 41.63 Å2 / CC1/2: 0.961 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.046 / Net I/σ(I): 17.1
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.633 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1142 / CC1/2: 0.838 / Rpim(I) all: 0.26 / % possible all: 99.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
HKL-2000data processing
CNSphasing
PHENIX1.13_2998refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 7D4S

7d4s


Resolution: 2.7→24.24 Å / SU ML: 0.3154 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.2236 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2498 571 4.91 %
Rwork0.1923 11070 -
obs0.1951 11641 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.8 Å2
Refinement stepCycle: LAST / Resolution: 2.7→24.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2773 0 62 206 3041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00192911
X-RAY DIFFRACTIONf_angle_d0.64823967
X-RAY DIFFRACTIONf_chiral_restr0.0396422
X-RAY DIFFRACTIONf_plane_restr0.0042501
X-RAY DIFFRACTIONf_dihedral_angle_d21.561741
LS refinement shellResolution: 2.7→2.97 Å
RfactorNum. reflection% reflection
Rfree0.2838 136 -
Rwork0.225 2625 -
obs--95.5 %
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)
11.218261328670.175621316609-0.1477425067570.6748412926580.5315763123590.6234318714820.0971628571602-0.1389586323350.2714765448820.113540755275-0.09628588409290.248809475512-0.331727257236-0.0236310242033-0.0001319142350690.2307582277090.0381617355023-0.02259220421610.225844767813-0.004450295176320.2787305881270.33731199074944.777218194750.9622729072
21.332897596420.181516117418-0.6880973612310.353268409727-0.4597574344920.814548415972-0.0364731715683-0.4176997800760.156505473059-0.04996255126520.01773634380180.0333309338003-0.05556326117570.0842202969783-0.0001084368848180.2455610447330.00776458397119-0.03610278374950.32780580817-0.07904337382180.2815672398977.1302438118338.868398118154.6651852793
30.966473245338-0.0746595247924-0.507494388610.6182527813810.1775489919521.20175324092-0.00186399883750.0830498939480.0469017096745-0.171613661109-0.0404086646067-0.037774211843-0.1326566964810.04684346712730.0001506477876960.232670459953-0.0116194511697-0.01600295719080.1682657717270.02353781267330.18252000806415.381053775840.512439265430.0983741214
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 99 )
2X-RAY DIFFRACTION2chain 'A' and (resid 100 through 220 )
3X-RAY DIFFRACTION3chain 'A' and (resid 221 through 354 )

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