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- PDB-7n34: Structure of Yersinia aleksiciae Cap15 cyclic dinucleotide recept... -

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Basic information

Entry
Database: PDB / ID: 7n34
TitleStructure of Yersinia aleksiciae Cap15 cyclic dinucleotide receptor, crystal form 1
ComponentsCap15
KeywordsIMMUNE SYSTEM / phage defense / CBASS / beta barrel
Biological speciesYersinia aleksiciae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsDuncan-Lowey, B. / McNamara-Bordewick, N.K. / Kranzusch, P.J.
CitationJournal: Mol.Cell / Year: 2021
Title: Effector-mediated membrane disruption controls cell death in CBASS antiphage defense.
Authors: Duncan-Lowey, B. / McNamara-Bordewick, N.K. / Tal, N. / Sorek, R. / Kranzusch, P.J.
History
DepositionMay 31, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 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 / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Dec 29, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Oct 30, 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

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Assembly

Deposited unit
A: Cap15


Theoretical massNumber of molelcules
Total (without water)15,0441
Polymers15,0441
Non-polymers00
Water43224
1
A: Cap15

A: Cap15


Theoretical massNumber of molelcules
Total (without water)30,0872
Polymers30,0872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area1480 Å2
ΔGint-12 kcal/mol
Surface area13120 Å2
MethodPISA
2
A: Cap15

A: Cap15


Theoretical massNumber of molelcules
Total (without water)30,0872
Polymers30,0872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area1370 Å2
ΔGint-8 kcal/mol
Surface area13230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.292, 31.039, 50.019
Angle α, β, γ (deg.)90.000, 100.225, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Cap15


Mass: 15043.534 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia aleksiciae (bacteria) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.37 Å3/Da / Density % sol: 48.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 40% PEG-200, 0.1 M N-(2-Acetamido)iminodiacetic acid pH 5.8

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.9→37.01 Å / Num. obs: 11344 / % possible obs: 99.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 41.53 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.029 / Net I/σ(I): 13.3
Reflection shellResolution: 1.9→1.94 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 719 / CC1/2: 0.562 / Rpim(I) all: 0.643

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→37.01 Å / SU ML: 0.237 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.9986
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2543 1134 10.02 %
Rwork0.2145 10183 -
obs0.2184 11317 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.87 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms869 0 0 24 893
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063889
X-RAY DIFFRACTIONf_angle_d0.75211197
X-RAY DIFFRACTIONf_chiral_restr0.0539125
X-RAY DIFFRACTIONf_plane_restr0.0044151
X-RAY DIFFRACTIONf_dihedral_angle_d17.5996312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.990.34671380.31431239X-RAY DIFFRACTION98.64
1.99-2.090.29671380.24441249X-RAY DIFFRACTION99.86
2.09-2.220.28821440.23121283X-RAY DIFFRACTION99.58
2.22-2.390.27711400.24671258X-RAY DIFFRACTION99.79
2.39-2.630.26681410.23541272X-RAY DIFFRACTION99.37
2.63-3.020.29771420.22181265X-RAY DIFFRACTION99.72
3.02-3.80.24181430.21041293X-RAY DIFFRACTION99.58
3.8-37.010.23191480.19691324X-RAY DIFFRACTION99.59
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)
14.01325523397-1.147511827833.314752479640.9570860618890.1209510449424.456843450150.287890522829-0.838283863029-0.9746968803230.359544901276-0.6825329770650.146672474893-0.198626798756-0.3905475546740.1964023991090.647127931395-0.04547698556540.06301003766930.6976508258730.135710051210.3601919752741.569795641219.728934422722.2303955435
23.426298664111.355829329352.599004325545.013011366822.90390532842.69386048823-0.09523684155980.4509198665080.12779637535-0.820405276335-0.2188558250440.313361987083-1.19263141572-1.454667985-0.02306111533190.4109476569560.128367308856-0.1092374697870.6071233290630.01464222936160.41876151567731.708827544115.8738213328-3.55587730509
31.679394586221.18480348588-0.6002276183812.341008904471.110656564541.6271783893-0.0776336931199-0.360687215608-0.3295268846830.5189019394160.06510342903630.385471748365-0.0906199832307-1.699089731220.0008922385141950.3496384446830.03224114781510.05413559109240.631563231184-0.073273057540.48178534066330.4989148512.5523534326.27150533407
41.25313854083-1.87610835996-1.267801978153.211993842761.40474409751.568584524690.16119156509-0.625096650229-0.4055451161770.896122052013-0.06003675060750.03010893689191.30634993602-0.93991230553-0.002085017111840.516912153735-0.06883681184120.0204723111120.5395298559030.06031625218750.3854864594636.20029155798.9409052772512.9605632823
55.43066798171-2.01081735661-1.664648091613.15942121425-2.644051675966.1978394134-0.0418893670958-0.432499821522-0.2921112759620.0648148950326-0.0430480365826-0.2496480813380.257644464057-0.2212362255670.001060005012570.386652513069-0.00385999446056-0.0003510499992250.271053978617-0.003081564028140.24992163163539.552672896613.12707369667.03783341999
62.98301180915-0.998515468717-0.7944479529562.56456872338-2.683308355824.157570417260.4151331330370.165674708451-0.2977390674280.9371512279090.0341081526362-1.094376619720.4744486332350.47943729918-0.003131930872980.3370855401030.02904370295040.03267809795810.3091932429450.004115135093390.33783518360741.424241824411.6875283736.03147583418
73.89925928279-2.62333725443-3.520609368552.74956898250.1681846553337.279020585520.1243454833660.0346259630156-0.749850974441-0.861586857428-0.314293070733-0.2444507585-0.805830581156-0.2393126255260.01722968975940.2975786244220.013228526629-0.03255708285160.4177217203080.0732753768040.40209599690440.351338438313.60142440293.09302908689
82.000373465368.15577916083-2.489335043977.23617064868-3.706563130583.873195691020.534535253476-0.05916527271283.122579223640.986686239657-1.046181026162.41106055701-2.55861135453-0.831987525186-0.02941740313680.854876097880.1187434266730.02434642941270.60229060757-0.1259806078030.56910262843134.213266300826.368053647712.3740176951
92.122420929460.8704266353272.314354958213.639900501580.8900141472624.98338326501-0.3763030944550.497096677214-0.12623109106-0.3228271036320.628875612417-0.325628691247-0.1574508798080.4107909945830.08339232950080.33442128130.0143609779026-0.08628444268730.3710098786860.07557206115690.34906220708139.774611524914.4286433515-2.63563694184
101.549082383660.1812680119241.146638413750.2895870389420.06297908082621.35845117073-0.5466042908090.2067852371890.102569355141-0.148913301361-0.0422503211180.380679881573-0.176925123801-0.151896475218-0.07662884909370.3897328625070.0754593121147-0.03934500463190.418699086543-0.02709009979130.50294490951733.201567950218.13494018871.74384839989
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 84 through 93 )84 - 931 - 10
22chain 'A' and (resid 94 through 108 )94 - 10811 - 25
33chain 'A' and (resid 109 through 119 )109 - 11926 - 36
44chain 'A' and (resid 120 through 128 )120 - 12837 - 45
55chain 'A' and (resid 129 through 147 )129 - 14746 - 64
66chain 'A' and (resid 148 through 157 )148 - 15765 - 74
77chain 'A' and (resid 158 through 177 )158 - 17775 - 83
88chain 'A' and (resid 178 through 182 )178 - 18284 - 88
99chain 'A' and (resid 183 through 196 )183 - 19689 - 99
1010chain 'A' and (resid 197 through 205 )197 - 205100 - 108

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