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- PDB-6e0l: Structure of Rhodothermus marinus CdnE c-UMP-AMP synthase with Ap... -

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Basic information

Entry
Database: PDB / ID: 6e0l
TitleStructure of Rhodothermus marinus CdnE c-UMP-AMP synthase with Apcpp and Upnpp
ComponentscGAS/DncV-like nucleotidyltransferase in E. coli homolog
KeywordsTRANSFERASE / cGAS / DncV / cyclic dinucleotide / nucleotide second messenger / nucleotidyltransferase
Function / homology
Function and homology information


nucleotide metabolic process / nucleotidyltransferase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / defense response to virus / ATP binding / metal ion binding
Similarity search - Function
2'-5'-oligoadenylate synthase N-terminal region profile. / 2-5OAS/ClassI-CCAase, nucleotidyltransferase domain / Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
Chem-2KH / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / Cyclic UMP-AMP synthase
Similarity search - Component
Biological speciesRhodothermus marinus SG0.5JP17-172 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsEaglesham, J.B. / Whiteley, A.T. / de Oliveira Mann, C.C. / Morehouse, B.R. / Nieminen, E.A. / King, D.S. / Lee, A.S.Y. / Mekalanos, J.J. / Kranzusch, P.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI018045 United States
CitationJournal: Nature / Year: 2019
Title: Bacterial cGAS-like enzymes synthesize diverse nucleotide signals.
Authors: Whiteley, A.T. / Eaglesham, J.B. / de Oliveira Mann, C.C. / Morehouse, B.R. / Lowey, B. / Nieminen, E.A. / Danilchanka, O. / King, D.S. / Lee, A.S.Y. / Mekalanos, J.J. / Kranzusch, P.J.
History
DepositionJul 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 27, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cGAS/DncV-like nucleotidyltransferase in E. coli homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9054
Polymers34,8921
Non-polymers1,0133
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.647, 65.652, 88.855
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein cGAS/DncV-like nucleotidyltransferase in E. coli homolog


Mass: 34892.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodothermus marinus SG0.5JP17-172 (bacteria)
Gene: Rhom172_2837 / Production host: Escherichia coli (E. coli) / References: UniProt: G2SLH8
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-2KH / 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

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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: 2.16 Å3/Da / Density % sol: 43.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 24% PEG-3350, 240 mM sodium malonate

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.25→36.92 Å / Num. obs: 14799 / % possible obs: 99.1 % / Redundancy: 5.3 % / Rpim(I) all: 0.068 / Net I/av σ(I): 9.8 / Net I/σ(I): 9.8
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 3 / Num. unique obs: 1263 / Rpim(I) all: 0.304 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.25→36.92 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.39
RfactorNum. reflection% reflectionSelection details
Rfree0.2166 740 5.01 %5
Rwork0.1819 ---
obs0.1836 14768 98.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.25→36.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2426 0 61 177 2664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082559
X-RAY DIFFRACTIONf_angle_d1.0913479
X-RAY DIFFRACTIONf_dihedral_angle_d12.581483
X-RAY DIFFRACTIONf_chiral_restr0.07346
X-RAY DIFFRACTIONf_plane_restr0.008441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2475-2.4210.28171410.21632691X-RAY DIFFRACTION97
2.421-2.66460.261470.20512791X-RAY DIFFRACTION100
2.6646-3.050.23611500.19542808X-RAY DIFFRACTION100
3.05-3.8420.19531480.16852816X-RAY DIFFRACTION99
3.842-36.92660.18621540.16512922X-RAY DIFFRACTION98
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)
10.23060.20420.14470.2520.21360.1658-0.03780.3574-0.1912-0.08690.1225-0.10230.00670.2169-0.0320.15320.0052-0.00930.1725-0.01230.125224.841630.055845.156
20.5061-0.019-0.09750.3851-0.13030.780.0436-0.00250.05030.01210.0017-0.0749-0.0844-0.0061-0.00940.0944-0.0048-0.00410.0786-0.00420.104534.148337.099764.8545
30.72650.23050.25680.59110.3030.49790.1283-0.1289-0.16350.1627-0.0884-0.06730.1456-0.08540.13440.1094-0.00160.00270.08450.01140.07725.738727.041567.6885
40.7184-0.47610.02420.3036-0.08140.3310.0792-0.04840.0289-0.0011-0.04110.05130.0283-0.04210.14920.0953-0.00890.01140.081-0.01260.11456.892227.435353.7649
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 32 )
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 126 )
3X-RAY DIFFRACTION3chain 'A' and (resid 127 through 185 )
4X-RAY DIFFRACTION4chain 'A' and (resid 186 through 293 )

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