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

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Basic information

Entry
Database: PDB / ID: 4txz
TitleCrystal structure of Vibrio cholerae DncV cyclic AMP-GMP synthase in complex with nonhydrolyzable GTP
ComponentsCyclic AMP-GMP synthase
KeywordsTRANSFERASE / nucleotidyl transferase / cyclic nucleotide synthase / cGAS
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
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 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 / Structure summary
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords
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 / _struct_keywords.text
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

Downloads & links

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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)95,0728
Polymers93,9332
Non-polymers1,1406
Water905
1
A: Cyclic AMP-GMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5364
Polymers46,9661
Non-polymers5703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cyclic AMP-GMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5364
Polymers46,9661
Non-polymers5703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.041, 59.373, 103.498
Angle α, β, γ (deg.)90.00, 96.04, 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-G2P / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-CPP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.28 Å3/Da / Density % sol: 46.01 %
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: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.8→45.19 Å / Num. obs: 20746 / % possible obs: 97.9 % / Redundancy: 3.5 % / Net I/σ(I): 5.8

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2.8→45.185 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2422 528 2.56 %10
Rwork0.2283 ---
obs0.2287 20664 97.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→45.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5884 0 68 5 5957
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036066
X-RAY DIFFRACTIONf_angle_d0.8028191
X-RAY DIFFRACTIONf_dihedral_angle_d18.4012321
X-RAY DIFFRACTIONf_chiral_restr0.031894
X-RAY DIFFRACTIONf_plane_restr0.0041045
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.08180.35511250.33134953X-RAY DIFFRACTION97
3.0818-3.52750.29621410.27655077X-RAY DIFFRACTION99
3.5275-4.44370.20851260.21294946X-RAY DIFFRACTION97
4.4437-45.19050.20211360.18465160X-RAY DIFFRACTION98
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)
12.32740.48230.81871.8292-0.67560.7028-0.43640.10530.19010.24860.150.34290.12991.0588-0.11570.43330.03490.02160.4234-0.00970.412512.941719.6638-35.8584
22.34290.44941.54953.33771.16814.79840.33441.2285-0.0543-0.13090.2015-0.16380.14740.8235-0.63030.3352-0.05520.03680.4010.05890.2615-8.38388.4214-65.8459
34.0616-1.23470.69652.57010.57483.3339-0.2840.4562-1.0028-0.14480.44970.96170.4066-0.6451-0.16350.5649-0.1724-0.03830.6529-0.02180.7975-24.4845-2.9336-69.5663
42.5277-0.01220.65582.61920.03984.1423-0.57660.20771.08540.19380.04710.6524-0.4088-0.322-0.00390.65290.01120.03680.5850.08060.7181-17.013615.4269-64.4788
50.373-0.1371.37511.6335-1.25943.902-0.0801-0.0513-0.1515-0.00350.03940.12470.0808-0.31040.21930.46740.01880.03470.3709-0.00170.4157-8.381312.7083-51.1173
60.9652-0.32291.33813.676-1.15921.7706-0.1561-0.1424-0.14010.58580.24040.2347-0.0205-0.1391-0.21410.4967-0.0150.05450.43270.03890.3536-11.73381.8765-55.5061
72.9825-1.56991.48563.1101-0.71543.7472-0.0472-0.39040.10250.2020.120.5412-0.8034-0.58450.2910.50750.0813-0.02480.58220.02370.5171-16.384519.008-56.9305
84.1427-0.19952.52651.64671.67633.298-0.46310.20070.1994-0.2160.16120.3852-0.0913-0.13640.26360.6480.17910.11080.53660.08910.6506-13.987622.7457-48.2217
92.8290.1497-0.83052.67840.28081.6827-0.0512-0.22730.20780.18070.24860.1665-0.2051-0.1081-0.10220.39060.0731-0.04180.42340.00770.3438-1.730423.1723-32.8464
102.3580.503-1.62947.1354-2.23377.534-0.1141-0.2128-0.1648-0.4872-0.04570.5635-0.0268-1.4204-0.19080.42260.1112-0.04590.67290.02730.5929-18.861122.4054-33.8853
116.17710.1950.01171.7509-0.96792.25840.1936-1.386-0.6767-0.0097-0.0656-0.04350.1134-0.5428-0.2060.51080.11090.02260.5750.04660.3229-3.999716.3921-23.1215
124.58780.86380.16764.0587-0.03662.34430.1019-0.874-0.24970.6337-0.0003-0.2232-0.13080.3104-0.07790.54770.11130.0380.5892-0.00060.414214.590716.9561-25.948
135.1108-1.6267-0.45035.21930.08642.15310.47690.1437-0.4582-0.0659-0.3788-0.3527-0.56860.09890.15470.3875-0.00870.00250.41670.05010.432720.349520.725-88.3977
141.50630.4477-0.37034.03352.03293.76980.18930.7582-0.3781-0.33140.2176-0.2691-0.20210.0678-0.3560.39360.0843-0.00050.36420.0510.3744-4.38319.7073-115.7459
153.1307-1.27592.7541.5927-0.39454.48630.2567-0.2771-0.4716-0.09430.05850.68290.2431-0.9041-0.61620.6189-0.1407-0.09850.8099-0.09950.9014-21.0822-1.3908-117.4382
162.9151.2155-0.06863.83760.14364.9871-0.94450.68910.9415-0.84720.28990.847-1.3516-0.05330.33360.78530.1325-0.16890.5924-0.12340.741-12.776516.8735-113.3349
172.11610.52261.7380.58430.09982.8745-0.06880.4733-0.07180.3476-0.13570.1937-0.32480.15610.03450.4972-0.0013-0.04420.3966-0.05430.6047-1.014513.8225-100.2135
182.9295-0.4550.56426.24921.98253.4064-0.1554-0.4693-0.32950.56850.18840.61190.2191-0.5869-0.07320.40590.0110.0850.514-0.01180.4097-6.7143.1847-104.919
194.11450.3220.50863.49232.3165.204-0.5262-0.00470.9027-0.2026-0.13150.5989-1.0046-0.98920.1960.63130.125-0.1650.5639-0.0540.6802-11.391519.4783-105.7452
204.31761.48881.81851.25580.86554.4294-0.56710.33380.2181-0.1980.10740.2734-0.5563-0.60850.37070.61020.24190.05390.6174-0.02390.6484-7.641924.2138-97.647
212.30420.33551.60713.76151.67333.14550.0599-0.2584-0.00280.4928-0.06010.2740.0747-0.1244-0.00560.3947-0.08980.01230.3891-0.03290.37186.162524.5615-83.7729
222.3483-1.10120.43696.3107-4.64973.84650.37050.01760.33790.19560.0761.1545-0.5928-1.4332-2.52390.6331-0.10440.17520.7646-0.16150.8137-10.861324.0951-83.0608
236.46020.45850.96272.9301-0.25682.27590.315-1.5647-0.3024-0.0442-0.4083-0.0984-0.2295-0.3299-0.19340.5557-0.15440.03810.61450.02430.35465.013517.9497-73.8043
244.12910.2085-0.30042.4211-0.37574.52130.4876-1.0991-0.36860.9799-0.2411-0.98820.36240.5385-0.16310.6692-0.0431-0.15990.68370.15450.670823.064817.9262-78.7775
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 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 189 )
7X-RAY DIFFRACTION7chain 'A' and (resid 190 through 249 )
8X-RAY DIFFRACTION8chain 'A' and (resid 250 through 278 )
9X-RAY DIFFRACTION9chain 'A' and (resid 279 through 339 )
10X-RAY DIFFRACTION10chain 'A' and (resid 340 through 361 )
11X-RAY DIFFRACTION11chain 'A' and (resid 362 through 382 )
12X-RAY DIFFRACTION12chain 'A' and (resid 383 through 413 )
13X-RAY DIFFRACTION13chain 'B' and (resid 5 through 26 )
14X-RAY DIFFRACTION14chain 'B' and (resid 27 through 60 )
15X-RAY DIFFRACTION15chain 'B' and (resid 61 through 94 )
16X-RAY DIFFRACTION16chain 'B' and (resid 95 through 118 )
17X-RAY DIFFRACTION17chain 'B' and (resid 119 through 151 )
18X-RAY DIFFRACTION18chain 'B' and (resid 152 through 189 )
19X-RAY DIFFRACTION19chain 'B' and (resid 190 through 249 )
20X-RAY DIFFRACTION20chain 'B' and (resid 250 through 278 )
21X-RAY DIFFRACTION21chain 'B' and (resid 279 through 339 )
22X-RAY DIFFRACTION22chain 'B' and (resid 340 through 361 )
23X-RAY DIFFRACTION23chain 'B' and (resid 362 through 382 )
24X-RAY DIFFRACTION24chain 'B' and (resid 383 through 413 )

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