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- PDB-4u0l: Structure of the Vibrio cholerae di-nucleotide cyclase (DncV) mut... -

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Basic information

Entry
Database: PDB / ID: 4u0l
TitleStructure of the Vibrio cholerae di-nucleotide cyclase (DncV) mutant D131A-D133A
ComponentsCyclic AMP-GMP synthase
KeywordsTRANSFERASE / Regulation / mutation
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
Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesVibrio cholerae El Tor N16961 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsXiang, Y. / Zhu, D.Y.
Funding support China, 2items
OrganizationGrant numberCountry
Junior Thousand Talents Program of China20131770418 China
NSSFZR2011CQ023 China
CitationJournal: Mol.Cell / Year: 2014
Title: Structural Biochemistry of a Vibrio cholerae Dinucleotide Cyclase Reveals Cyclase Activity Regulation by Folates.
Authors: Zhu, D. / Wang, L. / Shang, G. / Liu, X. / Zhu, J. / Lu, D. / Wang, L. / Kan, B. / Zhang, J.R. / Xiang, Y.
History
DepositionJul 12, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Oct 22, 2014Group: Database references
Revision 1.3Feb 4, 2015Group: Derived calculations
Revision 1.4Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / refine_hist
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _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
B: Cyclic AMP-GMP synthase


Theoretical massNumber of molelcules
Total (without water)95,3322
Polymers95,3322
Non-polymers00
Water7,728429
1
A: Cyclic AMP-GMP synthase


Theoretical massNumber of molelcules
Total (without water)47,6661
Polymers47,6661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cyclic AMP-GMP synthase


Theoretical massNumber of molelcules
Total (without water)47,6661
Polymers47,6661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.899, 59.774, 104.681
Angle α, β, γ (deg.)90.00, 96.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 47666.242 Da / Num. of mol.: 2 / Fragment: UNP residues 1-419 / Mutation: D131A, D133A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae El Tor N16961 (bacteria)
Gene: dncV, VC_0179 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KVG7, cyclic GMP-AMP synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 2.28 Å3/Da / Density % sol: 46.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100mM Imidazole, 0.2M CaCl2, 15% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.968 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 2.1→43.9 Å / Num. obs: 54543 / % possible obs: 98.6 % / Redundancy: 9.4 % / Net I/σ(I): 33.4

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→43.9 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.233 2571 5.1 %
Rwork0.1873 --
obs0.1896 50392 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→43.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6150 0 0 429 6579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086287
X-RAY DIFFRACTIONf_angle_d1.0868470
X-RAY DIFFRACTIONf_dihedral_angle_d14.2022409
X-RAY DIFFRACTIONf_chiral_restr0.067927
X-RAY DIFFRACTIONf_plane_restr0.0051093
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.099-2.13940.29031280.21942635X-RAY DIFFRACTION98
2.1394-2.18310.25051350.2172627X-RAY DIFFRACTION100
2.1831-2.23050.26571660.21612636X-RAY DIFFRACTION100
2.2305-2.28240.29491400.21392603X-RAY DIFFRACTION100
2.2824-2.33950.31171310.21332667X-RAY DIFFRACTION100
2.3395-2.40280.25791370.20132654X-RAY DIFFRACTION100
2.4028-2.47350.27071630.20272646X-RAY DIFFRACTION100
2.4735-2.55330.22521570.20132621X-RAY DIFFRACTION100
2.5533-2.64450.23341370.19632638X-RAY DIFFRACTION100
2.6445-2.75040.28851310.19542669X-RAY DIFFRACTION100
2.7504-2.87560.2731260.20772707X-RAY DIFFRACTION100
2.8756-3.02710.25881430.19662640X-RAY DIFFRACTION100
3.0271-3.21670.22771500.20222650X-RAY DIFFRACTION100
3.2167-3.4650.23881470.1872677X-RAY DIFFRACTION100
3.465-3.81350.21741240.1782688X-RAY DIFFRACTION100
3.8135-4.36490.22091640.16142675X-RAY DIFFRACTION100
4.3649-5.49760.1951440.15662681X-RAY DIFFRACTION100
5.4976-43.93620.19321480.18642707X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 63.8441 Å / Origin y: 8.1529 Å / Origin z: 177.4149 Å
111213212223313233
T0.2583 Å2-0.0269 Å2-0.0091 Å2-0.2345 Å2-0.0018 Å2--0.3002 Å2
L0.1139 °20.0072 °2-0.2278 °2-0.2132 °2-0.1967 °2--1.7192 °2
S-0.0123 Å °-0.0559 Å °-0.0028 Å °0.0277 Å °-0.0219 Å °-0.0916 Å °-0.0895 Å °0.2638 Å °0.0367 Å °
Refinement TLS groupSelection details: all

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