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- PDB-7r65: Crystal structure of a bacterial cyclic UMP synthase from Burkhol... -

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Basic information

Entry
Database: PDB / ID: 7r65
TitleCrystal structure of a bacterial cyclic UMP synthase from Burkholderia cepacia LK29
ComponentsAdenylate/guanylate cyclase
KeywordsTRANSFERASE / Cyclic nucleotide / nucleotidyltransferase / bacteriophage-defense / Pycsar
Function / homology
Function and homology information


uridylate cyclase / cyclic nucleotide biosynthetic process / adenylate cyclase activity / defense response to virus / intracellular signal transduction / nucleotide binding / metal ion binding / cytoplasm
Similarity search - Function
Adenylate and Guanylate cyclase catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Guanylate cyclase domain profile. / Nucleotide cyclase
Similarity search - Domain/homology
Biological speciesBurkholderia cepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsMorehouse, B.R. / Kranzusch, P.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM133063 United States
CitationJournal: Cell / Year: 2021
Title: Cyclic CMP and cyclic UMP mediate bacterial immunity against phages.
Authors: Tal, N. / Morehouse, B.R. / Millman, A. / Stokar-Avihail, A. / Avraham, C. / Fedorenko, T. / Yirmiya, E. / Herbst, E. / Brandis, A. / Mehlman, T. / Oppenheimer-Shaanan, Y. / Keszei, A.F.A. / ...Authors: Tal, N. / Morehouse, B.R. / Millman, A. / Stokar-Avihail, A. / Avraham, C. / Fedorenko, T. / Yirmiya, E. / Herbst, E. / Brandis, A. / Mehlman, T. / Oppenheimer-Shaanan, Y. / Keszei, A.F.A. / Shao, S. / Amitai, G. / Kranzusch, P.J. / Sorek, R.
History
DepositionJun 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 24, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenylate/guanylate cyclase
B: Adenylate/guanylate cyclase
C: Adenylate/guanylate cyclase
D: Adenylate/guanylate cyclase


Theoretical massNumber of molelcules
Total (without water)103,0784
Polymers103,0784
Non-polymers00
Water19,7981099
1
A: Adenylate/guanylate cyclase
B: Adenylate/guanylate cyclase


Theoretical massNumber of molelcules
Total (without water)51,5392
Polymers51,5392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-48 kcal/mol
Surface area18330 Å2
MethodPISA
2
C: Adenylate/guanylate cyclase
D: Adenylate/guanylate cyclase


Theoretical massNumber of molelcules
Total (without water)51,5392
Polymers51,5392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint-50 kcal/mol
Surface area18330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.145, 66.758, 92.350
Angle α, β, γ (deg.)90.000, 111.262, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Adenylate/guanylate cyclase


Mass: 25769.516 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cepacia (bacteria) / Gene: VL15_12785 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0J5ZXG5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1099 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 46.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M ammonium acetate, 0.1 M HEPES-KOH pH 7.5, and 29% PEG-3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.45→48.96 Å / Num. obs: 167231 / % possible obs: 99.7 % / Redundancy: 48.9 % / Biso Wilson estimate: 16.22 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.029 / Net I/σ(I): 16.8
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 40.6 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 7966 / CC1/2: 0.181 / Rpim(I) all: 0.872 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→45.22 Å / SU ML: 0.1504 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.4623
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1976 2000 1.2 %
Rwork0.1772 164623 -
obs0.1774 166623 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.77 Å2
Refinement stepCycle: LAST / Resolution: 1.45→45.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7208 0 0 1099 8307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00377441
X-RAY DIFFRACTIONf_angle_d0.63810136
X-RAY DIFFRACTIONf_chiral_restr0.06651141
X-RAY DIFFRACTIONf_plane_restr0.00381280
X-RAY DIFFRACTIONf_dihedral_angle_d12.72532650
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.480.27211350.261211109X-RAY DIFFRACTION94.27
1.48-1.520.21281420.229411675X-RAY DIFFRACTION99.75
1.52-1.570.22931420.205211758X-RAY DIFFRACTION99.76
1.57-1.620.21821440.193511759X-RAY DIFFRACTION99.82
1.62-1.680.19841420.184211767X-RAY DIFFRACTION99.83
1.68-1.740.21671430.184811784X-RAY DIFFRACTION99.96
1.74-1.820.21241440.183311755X-RAY DIFFRACTION99.94
1.82-1.920.23181430.182411818X-RAY DIFFRACTION99.77
1.92-2.040.19541430.17111726X-RAY DIFFRACTION99.39
2.04-2.20.18731430.168711818X-RAY DIFFRACTION99.96
2.2-2.420.23361440.17511865X-RAY DIFFRACTION99.92
2.42-2.770.19291440.176311825X-RAY DIFFRACTION99.82
2.77-3.490.18991440.177411890X-RAY DIFFRACTION99.94
3.49-45.220.17071470.162812074X-RAY DIFFRACTION99.81
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)
10.374752395493-0.03458066833830.006623153906810.1366790622390.040926667760.7998457241280.0207268895058-0.01239300451940.0520476093681-0.003076472397970.0141862263945-0.00401983025672-0.1094119259610.04405221382450.03796591027380.132889087991-0.01905900031520.01546360466880.0785207862483-0.01585448903620.11577542036810.100593325738.5497831926-11.0651332536
20.7674147945160.1625377245720.02242440490180.7169266924860.1570891740091.181779672230.03133327075360.041735945872-0.0288057895283-0.0487983430730.03963800419720.0333573308002-0.100025002937-0.07569891286180.1440121053830.1020465287320.02572770340230.002324247490210.0737180165364-0.004826853788770.0996023183511-5.5025873699236.3859110825-11.011065115
31.650554103320.5404181589640.1040174633570.1768044728790.02707813594210.02283331125290.1242685831830.462295658660.0360855301386-0.0378687540204-0.07865825480250.0281581702363-0.476886534917-0.5093328368340.05422731205170.317142081870.1250744788880.01421239811290.2491083138330.05218295606570.151146748578-5.0759785347338.4334976915-32.7342239347
40.142889447744-0.1032503239330.001668724221320.1292319086120.09140620907090.3257133731920.007484125951730.2504215215460.228111031789-0.0771099022046-0.119408657667-0.0470032088158-0.192536922270.290514942289-0.0007601355545620.203112726304-0.01181564816640.02825460771160.2126980662560.01145170439840.13531731773514.526480461331.5677841258-33.1777379865
5-0.00106865292228-0.0157263832150.003491046163910.203309081722-0.1856320945250.160165310866-0.0370314794152-0.0775887512594-0.02411980834410.0689783931045-0.01319920597980.0791129402957-0.0975864920152-0.1181454284697.5072227268E-60.184452778979-0.003517536949340.01829926838250.226938856951-0.001939225778280.12961563431511.896311245229.9244375893-1.50226699977
60.15976551039-0.2520019481870.07244351947520.37755069151-0.1429919619930.360056245063-0.006354516223170.02365702206510.0613565567467-0.0234043667123-0.03784370335330.0028143531713-0.05202004112420.0202125414086-4.95556578235E-50.118512231752-0.02692552339110.01317801685370.161728376957-0.01504310154350.11180123769419.80251822633.1519287692-8.61319458002
70.260647349227-0.21669740293-0.04119518559670.370097321706-0.1695505999480.228013721459-0.022054420333-0.086061031068-0.006147037215530.07214323788330.0646118564182-0.08950808622890.05029420262410.103905672802-0.0005435804302750.117419283162-0.0009405120455310.0063334283690.179961720393-0.008421982214280.092584376738922.822086370226.5239828151-0.931640462633
80.411827582162-0.007447558190660.2022010049230.054785020985-0.1581874070680.3898705465290.0677095537371-0.08099131326650.0391134022267-0.00384024976203-0.01757737773150.110248038519-0.145275924224-0.01597660098441.78674392739E-50.172913241164-0.01986696143220.02362389106110.157020478164-0.01144288994290.11780320902311.36251378328.5666892464-21.3403165794
90.288451622415-0.1729429912580.01126987962660.8025192689640.003711097280270.7857455162340.0931263622272-0.121512650403-0.2316499186590.0456891516774-0.0829518141177-0.1003722827380.41683236710.000315300853092-0.0008229001444430.2093258108535.62348143889E-5-0.01119272867370.1587431897940.01600057400660.15718081483922.629249625513.0862334081-9.040339054
100.529068190638-0.0289982468052-0.002051429973560.1088583150210.06007200280620.572815457131-0.00186105515889-0.0181716914483-0.098319520152-0.0178850736769-0.0006819575342280.003932212394860.03804880260380.0136228565788-0.0007795582476520.09587608504270.001947218935180.005598901006280.07401239334870.01681620409180.14471701886243.810647448627.745190762-39.8681987541
111.043797066570.05137533940980.1450013326580.3256850645890.009198022712750.588346101147-0.01705189260.0492805249713-0.144511833030.0009022398201060.06569411872730.105247444604-0.0511449255726-0.07908455438670.01206081068980.1212215733060.025202691175-0.003398826517450.104421075556-0.008352728128710.13549580625645.224428926730.7459786574-56.1808673782
121.09128040685-0.236248384516-0.08437782608580.604740618385-0.1988238427480.878976395160.0242772828450.0991605623091-0.0970794100263-0.0761658982405-0.00577203419578-0.0300048165688-0.02551864389650.06375690414850.0129150424290.11099891850.00987587317901-0.001602399807660.0858528310081-0.0297688471130.11092090427756.370427153429.3547273265-51.2779331854
130.803179539876-0.07949189449510.2478300969040.2370019897150.4224396076920.5039500332090.03962754758640.117888981362-0.2065432428440.0433572054098-0.0289939239740.07247876488190.16570089679-0.3068303051770.0494181967490.143594455509-0.00821122730586-0.01686655607760.168891208372-0.01451202161190.17368599013925.890342727932.3909854918-52.9053681093
140.1116163898970.1532969987880.07530280082310.2006073222070.1090474916350.04608292718170.02885729596650.257961926688-0.120006733927-0.09297382197170.0170029580887-0.08207308937370.02870122015510.170743159335-0.0001391553659020.136497011664-0.005913891740910.006664571138840.23132858159-0.002159002572080.17190124050651.129872122236.4613948482-33.5240401202
150.342979829684-0.2012272658990.1626227181860.3791783837650.2002193060420.1347400345990.0501986090720.0572054441661-0.0545010439869-0.0830407080342-0.0424611772020.01173219800660.0638821416356-0.00262013701344-4.25472429131E-50.113722402189-0.00132950212732-9.11246766266E-50.1589092312080.02720918029110.15459658369941.047907595533.1545020026-30.0240790769
160.2475742864690.1796229661830.09370743905150.4576839274780.3433221016040.346065270993-0.0254506952247-0.0124226650116-0.00704011067690.06373439065920.0307326768192-0.0558013279941-0.01187656694040.09034930277610.00284484081460.0697420874608-0.000990202923216-0.0005785887969250.1597210667790.01735174503740.11496606887446.255671870539.7723229549-23.7651529976
170.2241102984740.0652833850947-0.009407318852280.01127714791880.05552917765020.410955292858-0.0134923110130.0229536647724-0.185373367714-0.03890948327910.00286349355322-0.04177705309030.03941740378710.094549619089-7.71368915413E-60.126424760026-9.66234027436E-5-0.00598757680160.1572041444640.02354624411210.16560476868534.1651229837.7163495852-43.8537350226
180.947813017049-0.03591441796580.4579826156930.8912529834250.09097654929960.395697731817-0.102182702824-0.04227716058040.35058602760.139854041777-0.07121350155940.0181799819561-0.3373115967120.113339915589-0.01134947204270.170065890289-0.0157455038638-0.0237805910140.1309730023030.01178941401710.16752477713839.265037883553.2037895814-27.8911432246
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 85 )AA1 - 851 - 88
22chain 'A' and (resid 86 through 229 )AA86 - 22989 - 233
33chain 'B' and (resid 1 through 16 )BB1 - 161 - 16
44chain 'B' and (resid 17 through 45 )BB17 - 4517 - 46
55chain 'B' and (resid 46 through 64 )BB46 - 6447 - 65
66chain 'B' and (resid 65 through 106 )BB65 - 10666 - 108
77chain 'B' and (resid 107 through 149 )BB107 - 149109 - 151
88chain 'B' and (resid 150 through 179 )BB150 - 179152 - 181
99chain 'B' and (resid 180 through 229 )BB180 - 229182 - 231
1010chain 'C' and (resid 1 through 85 )CC1 - 851 - 88
1111chain 'C' and (resid 86 through 149 )CC86 - 14989 - 153
1212chain 'C' and (resid 150 through 229 )CC150 - 229154 - 233
1313chain 'D' and (resid 1 through 45 )DD1 - 451 - 45
1414chain 'D' and (resid 46 through 64 )DD46 - 6446 - 64
1515chain 'D' and (resid 65 through 106 )DD65 - 10665 - 106
1616chain 'D' and (resid 107 through 149 )DD107 - 149107 - 149
1717chain 'D' and (resid 150 through 179 )DD150 - 179150 - 179
1818chain 'D' and (resid 180 through 229 )DD180 - 229180 - 229

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