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- PDB-7rrw: Monomeric CRM197 expressed in E. coli -

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Basic information

Entry
Database: PDB / ID: 7rrw
TitleMonomeric CRM197 expressed in E. coli
ComponentsDiphtheria toxin
KeywordsTOXIN / inactivated diphtheria toxin / vaccine carrier / E. coli expression
Function / homology
Function and homology information


NAD+-diphthamide ADP-ribosyltransferase activity / toxin activity / extracellular space
Similarity search - Function
Diphtheria toxin, receptor-binding domain / Diphtheria toxin, receptor-binding domain superfamily / Diphtheria toxin, R domain / Diphtheria toxin (NAD+-dipthamide ADP-ribosyltransferase) / Diphtheria toxin, catalytic domain / Diphtheria toxin, C domain / Diphtheria toxin, translocation domain superfamily / Diphtheria toxin, T domain
Similarity search - Domain/homology
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGallagher, D.T. / Lees, A.
Funding support United States, 1items
OrganizationGrant numberCountry
Other government United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2023
Title: Monomeric crystal structure of the vaccine carrier protein CRM 197 and implications for vaccine development.
Authors: Gallagher, D.T. / Oganesyan, N. / Lees, A.
History
DepositionAug 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Diphtheria toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6062
Polymers58,4831
Non-polymers1221
Water7,638424
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.024, 81.671, 71.758
Angle α, β, γ (deg.)90.000, 110.870, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Diphtheria toxin /


Mass: 58483.422 Da / Num. of mol.: 1 / Fragment: engineered variant / Mutation: G52E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Plasmid: pET-15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5PY51
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 424 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.76 Å3/Da / Density % sol: 55.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 8 / Details: 12% (w/v) PEG 10000, 40 mM Ca Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03317 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 1.7→45.71 Å / Num. obs: 87511 / % possible obs: 93.1 % / Redundancy: 4.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.042 / Rrim(I) all: 0.092 / Net I/σ(I): 7.4
Reflection shellResolution: 1.7→1.77 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.41 / Num. unique obs: 410 / Rpim(I) all: 0.913 / Rrim(I) all: 0.98 / % possible all: 77.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
X-GENdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5i82

5i82


Resolution: 2→16 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.295 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.157 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2166 2222 5.2 %RANDOM
Rwork0.1783 ---
obs0.1804 40508 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 111.69 Å2 / Biso mean: 35.651 Å2 / Biso min: 16.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å2-1.63 Å2
2--0.55 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: final / Resolution: 2→16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3884 0 8 424 4316
Biso mean--50.61 45.07 -
Num. residues----506
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123969
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.635376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9325502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.98924.216185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95115676
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7631513
X-RAY DIFFRACTIONr_chiral_restr0.1150.2528
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022971
LS refinement shellResolution: 2→2.051 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 154 -
Rwork0.195 2994 -
all-3148 -
obs--99.71 %
Refinement TLS params.Method: refined / Origin x: -1.947 Å / Origin y: 32.603 Å / Origin z: 18.567 Å
111213212223313233
T0.0211 Å2-0.0066 Å20.0144 Å2-0.0205 Å2-0.0058 Å2--0.0607 Å2
L0.3767 °20.289 °20.2912 °2-0.8749 °20.4319 °2--0.6096 °2
S0.0391 Å °-0.0246 Å °0.0382 Å °0.1286 Å °-0.0688 Å °0.1381 Å °0.0513 Å °-0.0933 Å °0.0297 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 535
2X-RAY DIFFRACTION1A601

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