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- PDB-7d4s: apo-form cyclic trinucleotide synthase CdnD -

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Basic information

Entry
Database: PDB / ID: 7d4s
Titleapo-form cyclic trinucleotide synthase CdnD
ComponentsCyclic AMP-AMP-GMP synthase
KeywordsTRANSFERASE / substrate analogue 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
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / Cyclic AMP-AMP-GMP synthase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 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)45,4867
Polymers44,3791
Non-polymers1,1086
Water8,179454
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-6 kcal/mol
Surface area15750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.316, 116.432, 107.410
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-716-

HOH

21A-851-

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-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / 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: 2.34 Å3/Da / Density % sol: 47.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 5 mM AMPcPP, 10 mM GTP, 10 mM MgCl2, 0.2 M Na-malonate, pH 6.0, and 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: 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: 1.93→50 Å / Num. obs: 31398 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 20.3 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.03 / Net I/σ(I): 25.7
Reflection shellResolution: 1.93→2 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 3124 / CC1/2: 0.95 / Rpim(I) all: 0.205 / % possible all: 100

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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 7D4O

7d4o


Resolution: 1.93→33.5 Å / SU ML: 0.1884 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.9316 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.192 1531 4.94 %
Rwork0.1521 29487 -
obs0.1541 31018 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.9 Å2
Refinement stepCycle: LAST / Resolution: 1.93→33.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2790 0 66 454 3310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00792941
X-RAY DIFFRACTIONf_angle_d0.89694009
X-RAY DIFFRACTIONf_chiral_restr0.0527427
X-RAY DIFFRACTIONf_plane_restr0.0057508
X-RAY DIFFRACTIONf_dihedral_angle_d20.50321739
LS refinement shellResolution: 1.93→2 Å
RfactorNum. reflection% reflection
Rfree0.2247 121 -
Rwork0.1981 2316 -
obs--86.05 %
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)
10.6249695374920.247623306766-0.08331595882410.2783456708310.003261624534430.3641021476640.145280626881-0.006071975214810.192710659856-0.0540332227812-0.1006622043440.0929818298244-0.5244782566970.00193657903448-0.2590027717070.2942654502240.0177833210771-0.005405144597650.1264818696090.007945809121230.2126466148287.527470365552.26509202244.5830909516
20.4636725483490.0200897282391-0.1870201012850.2774625866920.238625937390.2934268302870.0214877226324-0.07590524231310.0978414649057-0.00264429485689-0.06229176178540.0906426624233-0.0927312192462-0.0705436172564-0.01402554905450.05085783576510.021120679172-0.01280964277720.0729090117427-0.01515717612760.0883530032935-2.0642530379739.41230342855.6289412825
30.306655295064-0.0306908371844-0.1864951586850.08719449494580.05497894732360.2947199699210.00189237484284-0.0700409385290.04513634489210.00745874077006-0.0387799672337-0.0010444903531-0.07146669561140.0449771893159-4.18365808172E-60.146130658062-0.0143495718698-0.01605457006110.129924035985-0.005235702868360.13482880964813.537732485939.015459890558.8158736959
40.557730380431-0.163754414076-0.1986265562290.4503566605690.05036878347180.5727857663710.04376691877470.144991984030.00859630542032-0.0703383253474-0.02967620797310.0418933483369-0.0778626470205-0.02713773013610.003511590182850.102992770837-0.00183060140497-0.01741455545220.1354474981920.002662068787890.088119681209116.365017435336.993316286932.9153077733
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 37 )
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 130 )
3X-RAY DIFFRACTION3chain 'A' and (resid 131 through 206 )
4X-RAY DIFFRACTION4chain 'A' and (resid 207 through 355 )

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