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- PDB-4u0m: Structure of the Vibrio cholerae di-nucleotide cyclase (DncV) mut... -

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Basic information

Entry
Database: PDB / ID: 4u0m
TitleStructure of the Vibrio cholerae di-nucleotide cyclase (DncV) mutant D193N in complex with ATP, GTP and 5MTHFGLU2
ComponentsCyclic AMP-GMP synthase
KeywordsTRANSFERASE / regulation / mutation
Function / homology
Function and homology information


3',3'-cyclic GMP-AMP synthase activity / diguanylate cyclase activity / cyclic nucleotide biosynthetic process / negative regulation of chemotaxis / 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
ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Chem-TLL / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesVibrio cholerae El Tor N16961 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhu, D. / Xiang, Y.
Funding support China, 2items
OrganizationGrant numberCountry
Junior Thousand Talents Program of China20131770418 China
NSSF 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 1.3Nov 8, 2023Group: 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_initial_refinement_model / pdbx_struct_oper_list / refine_hist / struct_conn
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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _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: Cyclic AMP-GMP synthase
B: Cyclic AMP-GMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,3479
Polymers97,6492
Non-polymers2,6987
Water6,792377
1
A: Cyclic AMP-GMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4685
Polymers48,8241
Non-polymers1,6434
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-13 kcal/mol
Surface area18140 Å2
MethodPISA
2
B: Cyclic AMP-GMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8794
Polymers48,8241
Non-polymers1,0553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-13 kcal/mol
Surface area18660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.898, 59.860, 104.185
Angle α, β, γ (deg.)90.00, 95.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 48824.410 Da / Num. of mol.: 2 / Fragment: UNP residues 1-419 / Mutation: D193N
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

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Non-polymers , 5 types, 384 molecules

#2: 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
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-TLL / N-[4-({[(6S)-2-amino-5-methyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-gamma-glutamyl-L-glutamic acid


Mass: 588.570 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H32N8O9
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.22 Å3/Da / Density % sol: 44.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% w/v PEG 3350, 200mM NaCl, 100mM Tris-HCl, 5mM GTP, 5mM ATP

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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: 2.3→103.7 Å / Num. obs: 38293 / % possible obs: 99.5 % / Redundancy: 3.3 % / Net I/σ(I): 12.9

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U0L

4u0l


Resolution: 2.3→42.568 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.253 1920 5.01 %
Rwork0.1988 --
obs0.2015 38293 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→42.568 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6219 0 170 377 6766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126605
X-RAY DIFFRACTIONf_angle_d0.7048948
X-RAY DIFFRACTIONf_dihedral_angle_d12.7912532
X-RAY DIFFRACTIONf_chiral_restr0.036960
X-RAY DIFFRACTIONf_plane_restr0.0021126
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.295-2.35240.34871300.24592445X-RAY DIFFRACTION94
2.3524-2.4160.27691590.2362567X-RAY DIFFRACTION100
2.416-2.48710.33291270.22912643X-RAY DIFFRACTION100
2.4871-2.56740.32281320.23042582X-RAY DIFFRACTION100
2.5674-2.65910.29531580.22022570X-RAY DIFFRACTION100
2.6591-2.76560.27831330.22342604X-RAY DIFFRACTION100
2.7656-2.89140.26291390.23092614X-RAY DIFFRACTION100
2.8914-3.04380.35021340.22212622X-RAY DIFFRACTION100
3.0438-3.23440.27851480.21752580X-RAY DIFFRACTION100
3.2344-3.48410.24181230.19962626X-RAY DIFFRACTION100
3.4841-3.83450.22331360.18432629X-RAY DIFFRACTION99
3.8345-4.38880.2431180.1712620X-RAY DIFFRACTION99
4.3888-5.52760.20471500.16322614X-RAY DIFFRACTION99
5.5276-42.57480.19461330.18432657X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 65.6854 Å / Origin y: 8.3343 Å / Origin z: 177.149 Å
111213212223313233
T0.1813 Å2-0.0287 Å2-0.0182 Å2-0.1434 Å20.0143 Å2--0.218 Å2
L0.152 °20.0378 °2-0.1738 °2-0.3161 °2-0.2071 °2--1.8644 °2
S-0.0015 Å °-0.0605 Å °-0.0016 Å °0.0344 Å °-0.0459 Å °-0.0986 Å °-0.1575 Å °0.2666 Å °0.0462 Å °
Refinement TLS groupSelection details: all

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