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- PDB-4u03: Structure of the vibrio cholerae di-nucleotide cyclase (DncV) in ... -

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Basic information

Entry
Database: PDB / ID: 4u03
TitleStructure of the vibrio cholerae di-nucleotide cyclase (DncV) in complex with GTP and 5MTHFGLU2
ComponentsCyclic AMP-GMP synthase
KeywordsTRANSFERASE / regulation
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
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: 2.041 Å
AuthorsZhu, D.Y. / Xiang, Y.
Funding support China, 2items
OrganizationGrant numberCountry
Junior Thousand Talents Program20131770418 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 11, 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_conn_angle / 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_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 / _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)101,01812
Polymers97,6512
Non-polymers3,36710
Water5,134285
1
A: Cyclic AMP-GMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5096
Polymers48,8251
Non-polymers1,6845
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-24 kcal/mol
Surface area18470 Å2
MethodPISA
2
B: Cyclic AMP-GMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5096
Polymers48,8251
Non-polymers1,6845
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-22 kcal/mol
Surface area17840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.623, 59.846, 104.053
Angle α, β, γ (deg.)90.00, 95.81, 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: 48825.398 Da / Num. of mol.: 2 / Fragment: UNP residues 1-419
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 BL21(DE3) (bacteria) / References: UniProt: Q9KVG7, cyclic GMP-AMP synthase
#2: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: 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.: 2 / Source method: obtained synthetically / Formula: C25H32N8O9
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20% w/v PEG 3350, 200mM NaCl, 5mM ATP, 5mM GTP

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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: 2.04→103 Å / Num. obs: 54229 / % possible obs: 99 % / Redundancy: 3.6 % / Net I/σ(I): 16.9

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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: 2.041→43.633 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2333 2754 5.08 %
Rwork0.1802 --
obs0.183 54229 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.041→43.633 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6214 0 216 285 6715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076605
X-RAY DIFFRACTIONf_angle_d1.1438943
X-RAY DIFFRACTIONf_dihedral_angle_d16.2582551
X-RAY DIFFRACTIONf_chiral_restr0.07959
X-RAY DIFFRACTIONf_plane_restr0.0041134
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0407-2.07590.32171210.24322445X-RAY DIFFRACTION95
2.0759-2.11360.30081160.21692608X-RAY DIFFRACTION100
2.1136-2.15430.25861320.20992527X-RAY DIFFRACTION100
2.1543-2.19820.29031480.20852583X-RAY DIFFRACTION100
2.1982-2.2460.2741350.20012569X-RAY DIFFRACTION100
2.246-2.29830.27121310.1982587X-RAY DIFFRACTION100
2.2983-2.35570.25741410.19272556X-RAY DIFFRACTION100
2.3557-2.41940.28681410.19342581X-RAY DIFFRACTION100
2.4194-2.49060.23781320.19132576X-RAY DIFFRACTION100
2.4906-2.5710.26071100.19982599X-RAY DIFFRACTION100
2.571-2.66290.25891340.20492578X-RAY DIFFRACTION100
2.6629-2.76950.27541460.2122578X-RAY DIFFRACTION100
2.7695-2.89550.28381540.20992554X-RAY DIFFRACTION100
2.8955-3.04810.30121480.20752585X-RAY DIFFRACTION100
3.0481-3.2390.23451410.20052570X-RAY DIFFRACTION100
3.239-3.4890.23731500.18372580X-RAY DIFFRACTION100
3.489-3.83990.22881300.16392614X-RAY DIFFRACTION100
3.8399-4.39510.18661440.14382580X-RAY DIFFRACTION100
4.3951-5.53560.16941540.13492608X-RAY DIFFRACTION100
5.5356-43.64290.17771460.15712597X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 64.2877 Å / Origin y: 8.5722 Å / Origin z: 176.361 Å
111213212223313233
T0.2356 Å2-0.0241 Å20.0045 Å2-0.1589 Å20.0037 Å2--0.2522 Å2
L0.1412 °20.0367 °2-0.1003 °2-0.1761 °2-0.148 °2--1.4644 °2
S-0.0081 Å °-0.04 Å °-0.002 Å °0.0135 Å °-0.0272 Å °-0.0485 Å °-0.1495 Å °0.1945 Å °0.0406 Å °
Refinement TLS groupSelection details: all

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