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- PDB-4xj1: Crystal structure of Vibrio cholerae DncV apo form -

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Basic information

Entry
Database: PDB / ID: 4xj1
TitleCrystal structure of Vibrio cholerae DncV apo 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 DncV-like, nucleotidyltransferase domain / Cyclic GMP-AMP synthase, C-terminal domain
Similarity search - Domain/homology
Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.77 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclic AMP-GMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2185
Polymers44,9701
Non-polymers2484
Water4,197233
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint12 kcal/mol
Surface area17490 Å2
Unit cell
Length a, b, c (Å)118.998, 50.742, 73.072
Angle α, β, γ (deg.)90.00, 93.07, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1113-

HOH

21A-1117-

HOH

31A-1182-

HOH

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Components

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


Mass: 44970.090 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: PEG3350, sodium fluoride, Bis-Tris propane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97906 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97906 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 42361 / % possible obs: 99.3 % / Redundancy: 15.3 % / Net I/σ(I): 60

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
SHARPphasing
RefinementResolution: 1.77→47.329 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2039 1945 4.71 %
Rwork0.1803 --
obs0.1814 41260 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.77→47.329 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2924 0 16 233 3173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012995
X-RAY DIFFRACTIONf_angle_d1.1374041
X-RAY DIFFRACTIONf_dihedral_angle_d13.0241120
X-RAY DIFFRACTIONf_chiral_restr0.049447
X-RAY DIFFRACTIONf_plane_restr0.005523
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7691-1.79070.26431350.26142496X-RAY DIFFRACTION87
1.7907-1.81340.28951280.23772829X-RAY DIFFRACTION99
1.8134-1.83720.25021520.22912759X-RAY DIFFRACTION99
1.8372-1.86240.26191330.22072832X-RAY DIFFRACTION99
1.8624-1.8890.25791380.20562815X-RAY DIFFRACTION99
1.889-1.91720.22861350.1942766X-RAY DIFFRACTION99
1.9172-1.94720.22241330.19922814X-RAY DIFFRACTION99
1.9472-1.97910.23221370.18432839X-RAY DIFFRACTION99
1.9791-2.01320.22821370.18462815X-RAY DIFFRACTION99
2.0132-2.04980.19171400.18872781X-RAY DIFFRACTION99
2.0498-2.08920.1941470.18262876X-RAY DIFFRACTION99
2.0892-2.13190.22321180.18352767X-RAY DIFFRACTION99
2.1319-2.17820.2241500.17642808X-RAY DIFFRACTION99
2.1782-2.22890.21911580.17262833X-RAY DIFFRACTION99
2.2289-2.28460.20111280.16992784X-RAY DIFFRACTION100
2.2846-2.34640.17911410.17452851X-RAY DIFFRACTION100
2.3464-2.41550.21931310.17062858X-RAY DIFFRACTION100
2.4155-2.49340.19881280.18072819X-RAY DIFFRACTION100
2.4934-2.58250.21951520.18332799X-RAY DIFFRACTION100
2.5825-2.68590.21691370.19132859X-RAY DIFFRACTION100
2.6859-2.80820.20561550.18952826X-RAY DIFFRACTION100
2.8082-2.95620.19531320.20392844X-RAY DIFFRACTION100
2.9562-3.14140.22971330.19782810X-RAY DIFFRACTION100
3.1414-3.38380.23251460.18632839X-RAY DIFFRACTION100
3.3838-3.72430.2171420.18252831X-RAY DIFFRACTION100
3.7243-4.26290.19521420.15362848X-RAY DIFFRACTION100
4.2629-5.36960.13361440.14742827X-RAY DIFFRACTION100
5.3696-47.34580.19371380.17852802X-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)
10.99480.9839-1.96441.5073-2.91133.64190.1384-0.5396-0.17740.135-0.4014-0.0544-0.14960.62620.22120.3958-0.1971-00.53760.06780.24141.949125.787471.9918
21.5705-1.08060.31031.5352-1.62423.75220.0252-0.5035-0.43540.1529-0.04290.38940.41760.06640.01040.3695-0.06960.05650.42360.03750.327339.459124.946364.0529
31.56090.7348-1.34251.3052-0.73354.57190.2004-0.4679-0.17160.2562-0.3290.10090.0861-0.05670.08370.2593-0.0733-0.02210.36250.05290.256138.147423.913865.067
42.49291.0958-0.46561.8952-0.39221.28080.05750.0257-0.05360.0096-0.09140.06660.0427-0.02570.03170.13380.0207-0.02620.1006-0.03630.132539.267835.337240.1382
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 117 )
2X-RAY DIFFRACTION2chain 'A' and (resid 118 through 150 )
3X-RAY DIFFRACTION3chain 'A' and (resid 151 through 277 )
4X-RAY DIFFRACTION4chain 'A' and (resid 278 through 412 )

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