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- PDB-4xj5: Crystal structure of Vibrio cholerae DncV 3'-deoxy GTP bound form -

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Basic information

Entry
Database: PDB / ID: 4xj5
TitleCrystal structure of Vibrio cholerae DncV 3'-deoxy GTP bound form
ComponentsCyclic AMP-GMP synthase
KeywordsTRANSFERASE / Cyclic GMP-AMP synthase / Bacterial virulence / nucleotidyltransferase
Function / homology
Function and homology information


3',3'-cyclic GMP-AMP synthase activity / cyclic nucleotide biosynthetic process / negative regulation of chemotaxis / diguanylate cyclase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / defense response to virus / GTP binding / ATP binding / metal ion binding
Similarity search - Function
: / : / Cyclic GMP-AMP synthase, C-terminal domain / : / Cyclic GMP-AMP synthase DncV-like, nucleotidyltransferase domain
Similarity search - Domain/homology
3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.552 Å
AuthorsKato, K. / Ishii, R. / Ishitani, R. / Nureki, O.
CitationJournal: Structure / Year: 2015
Title: Structural Basis for the Catalytic Mechanism of DncV, Bacterial Homolog of Cyclic GMP-AMP Synthase
Authors: Kato, K. / Ishii, R. / Hirano, S. / Ishitani, R. / Nureki, O.
History
DepositionJan 8, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Database references
Revision 1.2Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclic AMP-GMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,02016
Polymers44,3141
Non-polymers1,70715
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-22 kcal/mol
Surface area17040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.950, 50.060, 72.270
Angle α, β, γ (deg.)90.00, 93.40, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cyclic AMP-GMP synthase / c-AMP-GMP synthase / Dinucleotide cyclase DncV


Mass: 44313.566 Da / Num. of mol.: 1 / Fragment: UNP residues 1-215,242-412
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Strain: N16961 / Gene: dncV, VC_0179 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9KVG7, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases

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Non-polymers , 5 types, 255 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GH3 / 3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE


Type: RNA linking / Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: PEG3350, sodium fluoride, Bis-Tris propane / PH range: 5.5-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 60205 / % possible obs: 98.5 % / Redundancy: 3.6 % / Net I/σ(I): 17.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: SAD
Starting model: 4XJ1

4xj1


Resolution: 1.552→46.997 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1933 3018 5.02 %
Rwork0.1748 --
obs0.1757 60174 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.552→46.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2873 0 97 240 3210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123119
X-RAY DIFFRACTIONf_angle_d1.3384221
X-RAY DIFFRACTIONf_dihedral_angle_d12.4871158
X-RAY DIFFRACTIONf_chiral_restr0.061460
X-RAY DIFFRACTIONf_plane_restr0.006542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5518-1.5760.35291290.30522234X-RAY DIFFRACTION85
1.576-1.60180.28521330.25872466X-RAY DIFFRACTION94
1.6018-1.62950.23931430.24752592X-RAY DIFFRACTION99
1.6295-1.65910.24991190.2192600X-RAY DIFFRACTION100
1.6591-1.6910.26351520.21062632X-RAY DIFFRACTION100
1.691-1.72550.24711370.20642613X-RAY DIFFRACTION100
1.7255-1.76310.23651320.20662604X-RAY DIFFRACTION100
1.7631-1.80410.25461460.2012621X-RAY DIFFRACTION100
1.8041-1.84920.22571290.19882629X-RAY DIFFRACTION100
1.8492-1.89920.23551450.19382611X-RAY DIFFRACTION100
1.8992-1.95510.2361320.18342652X-RAY DIFFRACTION100
1.9551-2.01820.261470.17872565X-RAY DIFFRACTION99
2.0182-2.09030.17281270.17052654X-RAY DIFFRACTION100
2.0903-2.1740.20981460.16572619X-RAY DIFFRACTION100
2.174-2.27290.18281400.16512632X-RAY DIFFRACTION100
2.2729-2.39280.18881320.16852615X-RAY DIFFRACTION100
2.3928-2.54270.19271310.17362647X-RAY DIFFRACTION100
2.5427-2.7390.1891440.17142623X-RAY DIFFRACTION100
2.739-3.01460.17061420.18482651X-RAY DIFFRACTION100
3.0146-3.45070.19681360.16922648X-RAY DIFFRACTION100
3.4507-4.3470.16421370.15022652X-RAY DIFFRACTION99
4.347-47.0190.15951390.1662596X-RAY DIFFRACTION94
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)
11.11421.4009-2.55342.3105-3.92765.34380.2026-0.2951-0.11450.3881-0.2656-0.0374-0.51920.46770.04120.3676-0.1082-0.01740.33680.03490.197141.45828.215870.424
20.45990.4727-0.89780.8731-1.52263.11330.0144-0.248-0.19590.2412-0.1012-0.02740.00010.19780.08480.2664-0.0272-0.01770.25180.06540.232539.875624.176662.6597
31.9951.1415-0.4351.7675-0.30630.9430.0380.0942-0.05580.0034-0.03930.05240.0328-0.07190.00070.14380.0111-0.02570.1711-0.01680.139438.416535.077638.2762
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 93 )
2X-RAY DIFFRACTION2chain 'A' and (resid 94 through 293 )
3X-RAY DIFFRACTION3chain 'A' and (resid 294 through 412 )

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