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- PDB-7ljo: Structure of the Bacteroides fragilis CD-NTase CdnB in complex wi... -

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Basic information

Entry
Database: PDB / ID: 7ljo
TitleStructure of the Bacteroides fragilis CD-NTase CdnB in complex with ADP
ComponentsCD-NTase
KeywordsTRANSFERASE / cGAMP / CD-NTase / CBASS
Function / homologyADENOSINE-5'-DIPHOSPHATE / Uncharacterized protein
Function and homology information
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsGovande, A. / Lowey, B. / Eaglesham, J.B. / Whiteley, A.T. / Kranzusch, P.J.
CitationJournal: Cell Rep / Year: 2021
Title: Molecular basis of CD-NTase nucleotide selection in CBASS anti-phage defense.
Authors: Govande, A.A. / Duncan-Lowey, B. / Eaglesham, J.B. / Whiteley, A.T. / Kranzusch, P.J.
History
DepositionJan 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CD-NTase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9164
Polymers39,0371
Non-polymers8793
Water6,287349
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-19 kcal/mol
Surface area13620 Å2
Unit cell
Length a, b, c (Å)63.373, 69.610, 92.396
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein CD-NTase


Mass: 39037.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: M075_1299 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A016JNT0
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.62 Å3/Da / Density % sol: 52.98 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 10 mM TCEP-HCl, not adjusted for pH, 22% PEG-3350 / PH range: 3.5-5

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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 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.76→46.86 Å / Num. obs: 41249 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 26.8 Å2 / Rpim(I) all: 0.041 / Net I/σ(I): 10.6
Reflection shellResolution: 1.76→1.79 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2272 / CC1/2: 0.364 / Rpim(I) all: 0.836

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house model of the selenomethionine substituted protein, determined using SAD phasing

Resolution: 1.76→46.86 Å / SU ML: 0.1547 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.5644
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1948 1999 4.87 %
Rwork0.1782 39081 -
obs0.179 41080 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.64 Å2
Refinement stepCycle: LAST / Resolution: 1.76→46.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2356 0 55 349 2760
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00292468
X-RAY DIFFRACTIONf_angle_d0.78693346
X-RAY DIFFRACTIONf_chiral_restr0.043355
X-RAY DIFFRACTIONf_plane_restr0.0048425
X-RAY DIFFRACTIONf_dihedral_angle_d18.9056934
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.80.29861360.30062663X-RAY DIFFRACTION96.15
1.8-1.850.32851390.24872722X-RAY DIFFRACTION99.44
1.85-1.910.24211400.21352761X-RAY DIFFRACTION100
1.91-1.970.24611430.20442775X-RAY DIFFRACTION99.97
1.97-2.040.21711420.19012773X-RAY DIFFRACTION99.97
2.04-2.120.23611420.17752772X-RAY DIFFRACTION100
2.12-2.220.19571400.16952752X-RAY DIFFRACTION99.9
2.22-2.330.19711430.16582779X-RAY DIFFRACTION99.97
2.33-2.480.16951430.16972806X-RAY DIFFRACTION100
2.48-2.670.19541430.18392794X-RAY DIFFRACTION99.97
2.67-2.940.2051440.18012810X-RAY DIFFRACTION99.93
2.94-3.370.21791450.18032830X-RAY DIFFRACTION99.87
3.37-4.240.18431460.16432855X-RAY DIFFRACTION100
4.24-46.860.14741530.16862989X-RAY DIFFRACTION99.94
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)
1-0.00294855291951-0.0736811621650.05710919489341.475659611440.9370451009611.35115291471-0.04821168912170.01809749284650.00746048151814-0.2973681881720.0237028755622-0.000266762126675-0.276419987890.102502118588-8.37977936073E-50.23973326207-0.01559052390050.01174079339250.2190366685040.01779293932730.19060461621432.768105847624.293779763320.212427167
21.046926311990.436312042428-0.2758869279492.302484526670.7180178182582.124315321170.0214030035941-0.0234313225131-0.0180609600234-0.0609948324436-0.03299905441450.351024695696-0.247912169228-0.130175974399-0.004419117704830.2368596080930.0172083291751-0.004858876740270.191877988799-0.003513453391280.23475490473525.98310803514.562846401516.150032598
30.1912988868890.240428899275-0.07199964870350.579059755830.07083792325240.113160974040.04295335923950.1867649875050.00389094481001-0.0654325436356-0.09649292603760.212132502574-0.09821005175320.05806549443129.75357601957E-50.2129910190290.0162075223198-0.0204584516320.2396375984450.003949554569250.25433556823726.846186349429.416422010634.2368219591
41.332056647350.368022029488-0.1939460487681.48082455327-0.2334475816721.16569810814-0.0844562512367-0.10697425627-0.1151708595750.07254151112490.04406175675980.02203515809990.0279629292274-0.0277617560624-3.79426619265E-50.1841491322970.0223909539780.007597360739320.2071097147620.02594343145510.18673309841330.492835075523.085811973245.2739251859
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 1 through 85 )1 - 851 - 85
22chain 'A' and (resid 86 through 152 )86 - 15286 - 152
33chain 'A' and (resid 153 through 184 )153 - 184153 - 184
44chain 'A' and (resid 185 through 290 )185 - 290185 - 290

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