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- PDB-7n35: Structure of Yersinia aleksiciae Cap15 cyclic dinucleotide recept... -

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Basic information

Entry
Database: PDB / ID: 7n35
TitleStructure of Yersinia aleksiciae Cap15 cyclic dinucleotide receptor, crystal form 2
ComponentsCap15
KeywordsIMMUNE SYSTEM / phage defense / CBASS / beta barrel
Biological speciesYersinia aleksiciae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cap15
B: Cap15


Theoretical massNumber of molelcules
Total (without water)29,9932
Polymers29,9932
Non-polymers00
Water00
1
A: Cap15

B: Cap15


Theoretical massNumber of molelcules
Total (without water)29,9932
Polymers29,9932
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_445x-1,y-1,z1
Buried area1190 Å2
ΔGint-13 kcal/mol
Surface area13000 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-10 kcal/mol
Surface area12990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.866, 50.866, 155.018
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Protein Cap15


Mass: 14996.638 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia aleksiciae (bacteria) / Production host: Escherichia coli (E. coli)
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: 1.93 Å3/Da / Density % sol: 36.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 40% PEG-200, 0.1 M N-(2-Acetamido)iminodiacetic acid pH 5.3

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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: Dec 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.6→44.05 Å / Num. obs: 7040 / % possible obs: 100 % / Redundancy: 15.9 % / Biso Wilson estimate: 97.93 Å2 / CC1/2: 1 / Rpim(I) all: 0.018 / Net I/σ(I): 19.3
Reflection shellResolution: 2.6→2.72 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 853 / CC1/2: 0.512 / Rpim(I) all: 0.674

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7N34

7n34


Resolution: 2.6→44.05 Å / SU ML: 0.5648 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 48.1836
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.313 679 9.73 %
Rwork0.2974 6302 -
obs0.299 6981 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 108.24 Å2
Refinement stepCycle: LAST / Resolution: 2.6→44.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1687 0 0 0 1687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211727
X-RAY DIFFRACTIONf_angle_d0.49082328
X-RAY DIFFRACTIONf_chiral_restr0.0435244
X-RAY DIFFRACTIONf_plane_restr0.0039293
X-RAY DIFFRACTIONf_dihedral_angle_d12.5888604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.80.55971310.46951261X-RAY DIFFRACTION99.57
2.8-3.080.41381360.38381253X-RAY DIFFRACTION99.86
3.08-3.530.39851360.38321267X-RAY DIFFRACTION100
3.53-4.440.3271370.31891251X-RAY DIFFRACTION100
4.45-44.050.2621390.24841270X-RAY DIFFRACTION99.86
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)
19.81161088282-2.533107467442.198602714993.384675593972.906048637584.16329260167-0.5223669166131.8743329634-0.964253540699-1.668686667671.107419647851.61585475733-0.52415578868-1.363363022510.08387926435410.966216640411-0.140933383768-0.1319284597980.171505209448-0.2177696407471.0566628898713.2114092040.591835832596-12.4053116163
23.97429206192-3.89492773239-4.816449853743.698741132334.61280319545.75406647004-3.7787755269-1.358374116572.38610243258-1.429797870231.64381679052.56665390270.1887102673911.029879771760.2271182026711.55145532716-0.290599195702-0.02222598779131.585174545210.3251897680931.8156783225225.973143472921.5673019207-15.8947128767
34.709278216872.949844244810.5882922608121.926629230070.385632379961.44231258690.0933354674520.841849888615-0.519971244765-4.208088884960.681893821601-0.250734777212.30225384823-0.354236373840.03275322077261.395571840880.05838259382770.1099384797870.669934824138-0.01567364047610.94523817559819.051939627-1.02496705608-14.7186056344
45.80809867892-1.285485467791.891662859395.5427120082-2.354536690374.03753364526-0.09452706847820.009860016105860.1447184726070.62925474245-0.206675620267-0.463177392929-1.105465131771.28650849886-0.0008664964597821.1031638951-0.2217012752060.03377496349270.5283896390140.07312825339111.3262755125222.7043586423.70514432939-9.94172462438
52.016255559732.076638633881.940713279721.941487436873.688231742761.88960618567-3.01537307734-4.663103388923.763473515794.18595173304-3.763693062133.33772694549-3.96845156958-3.66134042891-5.436315794610.536888753646-0.08212720580160.2196053700550.9482525548790.3092745346251.287634216247.37837306694.97050368051-9.9930910569
60.779854151862-0.00223468166369-0.9422817752630.9169898851240.3782306298331.18793604845-2.2386012892-2.855025171631.96674090236-0.9424436154940.4124590451530.00532496532604-0.6988382754832.01865825582-0.0407587346171.43435125590.15424476233-0.06475702499281.228833770890.01851545803571.2148992448824.734007778313.1871988077-10.3917760924
71.51430253430.04126403994-0.8630960708274.246105651611.384927980522.29213777937-0.755250676991-0.0282238865113-0.496213001855-1.365749010261.08506252447-0.743333178858-0.0814956712485-0.5811025068540.4993154882031.09437566644-0.198267108767-0.1769661177070.7280077674070.03330046072430.85062352779414.697873798.21687858289-15.8983786107
80.504645011603-0.658074032240.9580700179431.60314701783-0.5740637460270.45500685829-0.8464713388520.1413626308820.3181258126020.5632936192321.588714271970.3742817486460.268535428442-0.3115439221730.09601701215941.09055151227-0.352226951799-0.05261428280291.477681433670.05304648144441.6692271705231.450211067321.86333531937.20094155777
99.9459627216.024614254099.403589153753.68737277645.779305322198.945038174782.63765650337-1.87672518087-1.1896738532-2.51440738813.18927413466-0.7817741615882.30701330596-3.808730348542.031000977881.936764435820.0193700762032-0.03445971101941.311766221360.425370131921.1722571327822.62265919-0.45898690478810.0579015913
102.85081511783-2.42925416861-0.9434863391381.901865226920.266307798394-0.110632731778-0.63081999212-0.955973306024-0.620887177062-0.201053142247-0.658816361555-1.944042121720.6407646275230.5362922768460.0001319132035690.942432558604-0.198740255701-0.0884626784051.102976095120.0837570638541.1632320791936.898520937815.39861418397.80315910142
114.592087024531.11186999119-0.4927729581462.78128955551.546965127289.46681323141-0.291801305180.1093530150940.384530222183-0.8135416504260.1106546769050.9186361372540.112872349904-0.126549505853-0.0005585393119090.915602703199-0.325947400984-0.141110298431.036292181190.2474836252911.6597761194429.350452095317.81787007090.929028828564
122.666261035151.12124339231-0.5820590717521.94288638841.315053040193.49430405028-0.487791213033-0.22816844523-0.288890474425-1.027329409970.8786816777511.212909947010.567973852142-0.0001503170083152.406133831780.841954632367-0.1296593331330.08640623409881.177626475850.5918972451841.6709425731726.363108151611.12389248516.78910018027
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 86 through 101 )AA86 - 1011 - 16
22chain 'A' and (resid 102 through 108 )AA102 - 10817 - 23
33chain 'A' and (resid 109 through 124 )AA109 - 12424 - 39
44chain 'A' and (resid 125 through 176 )AA125 - 17640 - 80
55chain 'A' and (resid 177 through 183 )AA177 - 18381 - 87
66chain 'A' and (resid 184 through 197 )AA184 - 19788 - 96
77chain 'A' and (resid 198 through 205 )AA198 - 20597 - 104
88chain 'B' and (resid 86 through 102 )BB86 - 1021 - 17
99chain 'B' and (resid 103 through 108 )BB103 - 10818 - 23
1010chain 'B' and (resid 109 through 132 )BB109 - 13224 - 47
1111chain 'B' and (resid 133 through 182 )BB133 - 18248 - 84
1212chain 'B' and (resid 183 through 205 )BB183 - 20585 - 104

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