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- PDB-4xj3: Crystal structure of Vibrio cholerae DncV GTP bound form -

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Basic information

Entry
Database: PDB / ID: 4xj3
TitleCrystal structure of Vibrio cholerae DncV 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 / diguanylate cyclase activity / negative regulation of chemotaxis / cyclic nucleotide biosynthetic process / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / defense response to virus / GTP binding / ATP binding / metal ion binding
Similarity search - Function
: / : / : / Cyclic GMP-AMP synthase DncV-like, nucleotidyltransferase domain / Cyclic GMP-AMP synthase, C-terminal domain
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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.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

Downloads & links

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Assembly

Deposited unit
A: Cyclic AMP-GMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,96714
Polymers44,3141
Non-polymers1,65413
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-11 kcal/mol
Surface area17130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.780, 49.850, 72.860
Angle α, β, γ (deg.)90.00, 93.48, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1112-

HOH

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Components

#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
#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 / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.43 Å3/Da / Density % sol: 49.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: PEG3350, sodium fluoride, Bis-Tris propane / PH range: 6.0 - 6.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 49988 / % possible obs: 97.2 % / Redundancy: 3.8 % / Net I/σ(I): 10.15

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Processing

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

4xj1


Resolution: 1.65→45.953 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2069 2513 5.03 %
Rwork0.1755 --
obs0.1771 49987 97.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→45.953 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2907 0 102 263 3272
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073095
X-RAY DIFFRACTIONf_angle_d1.1024181
X-RAY DIFFRACTIONf_dihedral_angle_d16.5041167
X-RAY DIFFRACTIONf_chiral_restr0.042456
X-RAY DIFFRACTIONf_plane_restr0.004527
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.68170.31971190.27222086X-RAY DIFFRACTION78
1.6817-1.7160.27341380.25512509X-RAY DIFFRACTION93
1.716-1.75330.24131280.21792636X-RAY DIFFRACTION98
1.7533-1.79410.22471480.20862620X-RAY DIFFRACTION98
1.7941-1.8390.23671400.20152672X-RAY DIFFRACTION98
1.839-1.88870.27161280.18692635X-RAY DIFFRACTION98
1.8887-1.94430.24241490.19152621X-RAY DIFFRACTION98
1.9443-2.00710.21021330.18742685X-RAY DIFFRACTION98
2.0071-2.07880.20771570.17752662X-RAY DIFFRACTION98
2.0788-2.1620.2041320.16882650X-RAY DIFFRACTION99
2.162-2.26040.19541410.16262683X-RAY DIFFRACTION99
2.2604-2.37960.21741460.16962683X-RAY DIFFRACTION99
2.3796-2.52870.19631400.17212674X-RAY DIFFRACTION99
2.5287-2.72390.21611400.17252695X-RAY DIFFRACTION99
2.7239-2.9980.1891420.18962694X-RAY DIFFRACTION99
2.998-3.43160.19831430.17762723X-RAY DIFFRACTION99
3.4316-4.3230.20011420.15632753X-RAY DIFFRACTION100
4.323-45.97110.18371470.1582793X-RAY DIFFRACTION99
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)
10.95131.0428-2.00421.7266-2.99624.40260.1903-0.3048-0.1130.4253-0.242-0.0424-0.59910.42030.02380.3317-0.0923-0.02010.28740.04180.186641.25228.062771.9942
21.06040.0659-0.77030.7471-1.42643.03510.0568-0.2724-0.25630.2042-0.11860.0824-0.02540.21770.04350.2846-0.0552-0.00470.23930.05860.227837.880123.12768.3881
31.56740.5315-0.32421.3569-0.19421.04540.05520.0076-0.0720.0367-0.07190.0170.03350.00930.01470.08110.0086-0.01860.076-0.00830.097640.260533.253940.8339
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 260 )
3X-RAY DIFFRACTION3chain 'A' and (resid 261 through 412 )

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