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- PDB-4ty0: Crystal structure of Vibrio cholerae DncV cyclic AMP-GMP synthase... -

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Basic information

Entry
Database: PDB / ID: 4ty0
TitleCrystal structure of Vibrio cholerae DncV cyclic AMP-GMP synthase in complex with linear intermediate 5' pppA(3',5')pG
ComponentsCyclic AMP-GMP synthase
KeywordsTRANSFERASE / nucleotidyl transferase / cyclic nucleotide synthase / cGAS
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
Chem-38V / ACETATE ION / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsKranzusch, P.J. / Lee, A.S.Y. / Wilson, S.C. / Solovykh, M.S. / Vance, R.E. / Berger, J.M. / Doudna, J.A.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
G. Harold and Leila Y. Mathers Foundation United States
CitationJournal: Cell / Year: 2014
Title: Structure-Guided Reprogramming of Human cGAS Dinucleotide Linkage Specificity.
Authors: Kranzusch, P.J. / Lee, A.S. / Wilson, S.C. / Solovykh, M.S. / Vance, R.E. / Berger, J.M. / Doudna, J.A.
History
DepositionJul 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Feb 4, 2015Group: Derived calculations
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Dec 27, 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 / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)95,90811
Polymers93,9332
Non-polymers1,9759
Water9,548530
1
A: Cyclic AMP-GMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0427
Polymers46,9661
Non-polymers1,0766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cyclic AMP-GMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8654
Polymers46,9661
Non-polymers8993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.329, 59.596, 102.163
Angle α, β, γ (deg.)90.00, 96.47, 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: 46966.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: dncV, VC_0179 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KVG7, cyclic GMP-AMP synthase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-38V / [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3-[[(2R,3S,4R,5R)-5-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-4-oxidanyl-oxolan-2-yl]methoxy-[[oxidanyl(phosphonooxy)phosphoryl]methyl]phosphinic acid


Mass: 850.414 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N10O19P4
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 530 / 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: 2.26 Å3/Da / Density % sol: 45.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 30 mM HEPES-KOH pH 7.5, 200-300 mM Mg(OAc)2 and 20-22% PEG-3350

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.2818 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2818 Å / Relative weight: 1
ReflectionResolution: 1.8→45.345 Å / Num. obs: 76362 / % possible obs: 97.2 % / Redundancy: 7.4 % / Net I/σ(I): 9.7

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 1.8→45.345 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2059 1931 2.58 %10
Rwork0.1726 ---
obs0.1734 74879 95.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→45.345 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5967 0 124 530 6621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096209
X-RAY DIFFRACTIONf_angle_d1.2018390
X-RAY DIFFRACTIONf_dihedral_angle_d17.0522413
X-RAY DIFFRACTIONf_chiral_restr0.052913
X-RAY DIFFRACTIONf_plane_restr0.0061065
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8450.40021010.39213810X-RAY DIFFRACTION71
1.845-1.89490.35781320.34794990X-RAY DIFFRACTION93
1.8949-1.95070.33411380.29395221X-RAY DIFFRACTION97
1.9507-2.01360.27821390.24655264X-RAY DIFFRACTION97
2.0136-2.08560.24141390.22125249X-RAY DIFFRACTION97
2.0856-2.16910.2431400.19575263X-RAY DIFFRACTION98
2.1691-2.26780.23681410.17785336X-RAY DIFFRACTION98
2.2678-2.38740.18451400.17035292X-RAY DIFFRACTION98
2.3874-2.53690.19391410.16635334X-RAY DIFFRACTION99
2.5369-2.73280.2031420.16875349X-RAY DIFFRACTION98
2.7328-3.00780.19291420.17025390X-RAY DIFFRACTION99
3.0078-3.44290.20891440.16025418X-RAY DIFFRACTION99
3.4429-4.33710.18191440.13755453X-RAY DIFFRACTION99
4.3371-45.35970.16671480.14725579X-RAY DIFFRACTION100
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)
12.67590.2115-0.53482.63560.31632.6524-0.02090.2927-0.0979-0.09410.08380.2444-0.0222-0.2275-0.09780.2112-0.0179-0.00370.2211-0.0160.271562.381548.424-17.0344
24.956-1.532.57852.3454-1.38213.8190.05-0.50560.05630.03440.1452-0.0004-0.0286-0.1748-0.13450.24570.02290.0480.257-0.03920.192784.063636.688614.3241
33.54931.09281.24392.8976-0.172.6091-0.0251-0.2071-0.5630.04710.1585-0.67330.16010.416-0.08830.24650.06730.00740.456-0.00040.4357100.294925.345117.6797
43.9853-3.34064.56443.3816-2.91877.54-0.4546-0.15420.48110.36890.1259-0.5049-0.48310.36370.31060.2811-0.05340.01570.3309-0.06350.27892.752343.702812.981
51.47260.20811.21211.07720.19562.15090.0128-0.1218-0.0664-0.03230.0201-0.0060.01350.1804-0.01130.3037-0.01140.03130.2537-0.02120.225183.094440.9025-0.7249
61.21420.3322-0.31671.9071-0.65011.41680.03480.01570.1085-0.00360.0159-0.0108-0.10990.1925-0.02430.26060.00160.02630.2479-0.01970.218288.066437.77566.4501
72.87951.2107-0.90724.0703-0.04594.3681-0.113-0.21120.4769-0.31220.225-0.2942-0.58460.2819-0.23210.3612-0.045-0.02840.4112-0.03450.326995.630549.20023.9085
82.1702-0.14370.47961.8762-0.53181.4561-0.05490.03370.37920.08520.0516-0.0893-0.33450.0404-0.00750.2749-0.0264-0.00460.1901-0.00280.262978.24253.0446-15.2974
91.86560.81620.10752.83812.70737.34680.09520.1106-0.08290.22010.1111-0.26-0.4020.8531-0.24190.3161-0.106-0.01110.3925-0.02580.352494.450651.1458-17.0052
102.5418-1.23191.63782.2622-0.02281.45530.02550.7516-0.1729-0.15540.0521-0.0035-0.15690.2475-0.05310.3519-0.02350.01560.36220.00820.213179.803144.8782-27.9932
113.3478-0.1134-1.0252.4528-0.67823.84750.28470.5833-0.2682-0.4033-0.12270.57130.1655-0.5662-0.15010.3278-0.011-0.07010.3318-0.04180.325261.138845.3379-25.445
122.4756-0.0264-0.20941.8702-0.01143.14350.06460.1969-0.1537-0.14710.00460.3385-0.0784-0.2861-0.08360.2090.0053-0.00730.225-0.03840.265455.168649.073436.1119
134.4615-0.38341.46552.6323-0.80632.6187-0.1959-0.4014-0.11330.43330.1441-0.1361-0.25750.00140.06850.2630.011-0.01430.21680.01190.178579.392938.102363.7335
143.72230.37542.99281.8031-0.1625.75340.07140.0925-0.43220.0313-0.0133-0.77820.23980.86570.06070.30210.111-0.06090.59830.11920.529796.186627.265765.5006
153.3224-1.35531.39512.0503-0.78093.4559-0.3948-0.54850.71620.8858-0.1081-0.9202-0.80740.47930.27090.4231-0.1866-0.27360.3990.05090.482687.688845.423861.6001
161.4049-1.35091.08031.9027-1.14092.4810.015-0.02660.04410.0619-0.1273-0.04560.04960.14660.10730.2235-0.01470.02960.22230.01110.21975.379541.846847.7869
173.11510.6957-0.1662.7713-1.29162.28450.05870.1431-0.0861-0.1465-0.1337-0.24850.05650.3510.04970.20180.02860.02810.23940.01090.235281.974531.648552.8985
184.28164.3572.08389.42183.83833.6404-0.1975-0.21880.3598-0.0758-0.0403-0.5423-0.39280.5106-0.14240.3099-0.0593-0.06440.36870.05290.357985.404947.450854.2423
190.9723-1.21291.37152.9324-1.60272.9083-0.09280.21380.36160.2077-0.2535-0.5857-0.24760.64120.22950.2412-0.09990.01550.3390.0470.323583.387252.257446.0878
201.63530.0897-0.18863.2385-0.37132.12620.07650.18850.1412-0.2329-0.074-0.0788-0.091-0.0037-0.00790.20620.02450.01230.20380.03160.17469.662453.026131.6821
211.40220.1087-0.12782.13782.00776.56610.1747-0.10190.0479-0.1190.1421-0.7547-0.32251.2105-0.44440.2863-0.02820.06260.42620.04340.414286.626952.556531.7503
229.1794-3.19230.76932.6389-0.61241.87160.26930.58790.0906-0.4757-0.3448-0.02370.06760.06820.05380.42260.06670.01070.336-0.02470.212570.745446.395821.918
230.59130.4826-0.75542.4058-1.48324.04430.29820.5883-0.5354-0.6145-0.18430.73650.5569-0.704-0.12340.37520.0252-0.14120.3902-0.1110.372553.004645.21826.6261
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 60 )
3X-RAY DIFFRACTION3chain 'A' and (resid 61 through 94 )
4X-RAY DIFFRACTION4chain 'A' and (resid 95 through 118 )
5X-RAY DIFFRACTION5chain 'A' and (resid 119 through 151 )
6X-RAY DIFFRACTION6chain 'A' and (resid 152 through 214 )
7X-RAY DIFFRACTION7chain 'A' and (resid 215 through 261 )
8X-RAY DIFFRACTION8chain 'A' and (resid 262 through 339 )
9X-RAY DIFFRACTION9chain 'A' and (resid 340 through 361 )
10X-RAY DIFFRACTION10chain 'A' and (resid 362 through 382 )
11X-RAY DIFFRACTION11chain 'A' and (resid 383 through 413 )
12X-RAY DIFFRACTION12chain 'B' and (resid 5 through 26 )
13X-RAY DIFFRACTION13chain 'B' and (resid 27 through 60 )
14X-RAY DIFFRACTION14chain 'B' and (resid 61 through 94 )
15X-RAY DIFFRACTION15chain 'B' and (resid 95 through 118 )
16X-RAY DIFFRACTION16chain 'B' and (resid 119 through 151 )
17X-RAY DIFFRACTION17chain 'B' and (resid 152 through 189 )
18X-RAY DIFFRACTION18chain 'B' and (resid 190 through 246 )
19X-RAY DIFFRACTION19chain 'B' and (resid 247 through 278 )
20X-RAY DIFFRACTION20chain 'B' and (resid 279 through 340 )
21X-RAY DIFFRACTION21chain 'B' and (resid 341 through 361 )
22X-RAY DIFFRACTION22chain 'B' and (resid 362 through 382 )
23X-RAY DIFFRACTION23chain 'B' and (resid 383 through 411 )

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