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- PDB-9erv: Structure of Salmonella CapRel bound to Bas11 Gp54 -

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Basic information

Entry
Database: PDB / ID: 9erv
TitleStructure of Salmonella CapRel bound to Bas11 Gp54
Components
  • GP54
  • RelA/SpoT family protein
KeywordsRNA BINDING PROTEIN / tRNA pyrophosphokinase / activated enzyme complex
Function / homologyADENOSINE-5'-TRIPHOSPHATE
Function and homology information
Biological speciesSalmonella (bacteria)
Bacteriophage sp. (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.253 Å
AuthorsGarcia-Pino, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)864311European Union
CitationJournal: Nature / Year: 2024
Title: A bacterial immunity protein directly senses two disparate phage proteins.
Authors: Zhang, T. / Cepauskas, A. / Nadieina, A. / Thureau, A. / Coppieters 't Wallant, K. / Martens, C. / Lim, D.C. / Garcia-Pino, A. / Laub, M.T.
History
DepositionMar 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Database references / Category: struct_ref / struct_ref_seq
Item: _struct_ref.db_code / _struct_ref.db_name ..._struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 1.2Dec 4, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RelA/SpoT family protein
B: GP54
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3286
Polymers51,6812
Non-polymers6474
Water6,377354
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-44 kcal/mol
Surface area19630 Å2
Unit cell
Length a, b, c (Å)49.695, 103.264, 209.235
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein RelA/SpoT family protein


Mass: 42710.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella (bacteria) / Gene: J46_0058
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Protein GP54


Mass: 8971.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteriophage sp. (virus)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Non-polymers , 5 types, 358 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.01 Å3/Da / Density % sol: 59.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 25% PEG 1500 / PH range: 7.5-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Mar 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.25→50.13 Å / Num. obs: 22597 / % possible obs: 90.5 % / Redundancy: 9.4 % / Biso Wilson estimate: 34.69 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.27 / Rpim(I) all: 0.09 / Net I/σ(I): 9.1
Reflection shellResolution: 2.25→2.36 Å / Num. unique obs: 1611 / CC1/2: 0.29

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (24-FEB-2021)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.253→50.13 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.891 / SU R Cruickshank DPI: 0.297 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.345 / SU Rfree Blow DPI: 0.235 / SU Rfree Cruickshank DPI: 0.226
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1127 4.99 %RANDOM
Rwork0.1988 ---
obs0.2011 22597 86.9 %-
Displacement parametersBiso mean: 32.03 Å2
Baniso -1Baniso -2Baniso -3
1--1.8625 Å20 Å20 Å2
2--2.2246 Å20 Å2
3----0.3621 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.253→50.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3097 0 39 353 3489
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083187HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.924288HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1175SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes537HARMONIC5
X-RAY DIFFRACTIONt_it3182HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.02
X-RAY DIFFRACTIONt_other_torsion19.23
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion421SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2618SEMIHARMONIC4
LS refinement shellResolution: 2.253→2.29 Å
RfactorNum. reflection% reflection
Rfree0.3598 -3.54 %
Rwork0.2879 436 -
obs--40.79 %
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)
11.0210.30570.06660.34120.0280.3952-0.00290.03310.0139-0.0210.01650.0101-0.01490.0074-0.0136-0.05010.00930.0004-0.0248-0.0147-0.040111.437372.395184.0008
23.2254-0.3677-0.30691.93491.33616.93380.0161-0.042-0.10050.04820.1333-0.11150.5420.2764-0.1494-0.0888-0.0069-0.0116-0.0468-0.0014-0.19491.347459.153265.7593
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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