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- PDB-5i82: First Crystal Structure of E.coli Based Recombinant Diphtheria To... -

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Basic information

Entry
Database: PDB / ID: 5i82
TitleFirst Crystal Structure of E.coli Based Recombinant Diphtheria Toxin Mutant CRM197
ComponentsDiphtheria toxin
KeywordsTRANSFERASE / Diphtheria Toxin / CRM197 / CSGID / Recombinant / Structural Genomics / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


NAD+-diphthamide ADP-ribosyltransferase / NAD+-diphthamide ADP-ribosyltransferase activity / toxin activity / extracellular space / identical protein binding
Similarity search - Function
Diphtheria toxin, receptor-binding domain / 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 / Diphtheria Toxin; domain 1 ...Diphtheria toxin, receptor-binding domain / 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 / Diphtheria Toxin; domain 1 / Diphtheria Toxin, domain 1 / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Diphtheria toxin / Diphtheria toxin
Similarity search - Component
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsMinasov, G. / Shuvalova, L. / Mishra, R.P.N. / Goel, A. / Dubrovska, I. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Biosci.Rep. / Year: 2018
Title: Structural and immunological characterization of E. coli derived recombinant CRM 197 protein used as carrier in conjugate vaccines.
Authors: Mishra, R.P.N. / Yadav, R.S.P. / Jones, C. / Nocadello, S. / Minasov, G. / Shuvalova, L.A. / Anderson, W.F. / Goel, A.
History
DepositionFeb 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Diphtheria toxin
B: Diphtheria toxin
C: Diphtheria toxin
D: Diphtheria toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,3148
Polymers233,9344
Non-polymers3804
Water6,323351
1
A: Diphtheria toxin
B: Diphtheria toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,1554
Polymers116,9672
Non-polymers1882
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7760 Å2
ΔGint-41 kcal/mol
Surface area43240 Å2
MethodPISA
2
C: Diphtheria toxin
D: Diphtheria toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,1594
Polymers116,9672
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7830 Å2
ΔGint-56 kcal/mol
Surface area42990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.214, 69.167, 127.882
Angle α, β, γ (deg.)90.09, 90.01, 82.02
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Diphtheria toxin /


Mass: 58483.422 Da / Num. of mol.: 4 / Mutation: G52E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Plasmid: pBioE / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: Q5PY51, UniProt: Q6NK15*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O

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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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein: 22.9 mg/ml, 0.15M Sodium chloride,0.01M Tris-HCL (pH 8.3); Screen: Classics II (G2), 0.2M Lithium sulfate, 0.1M Bis-Tris (pH 5.5), 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 13, 2015
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 98137 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Biso Wilson estimate: 57.5 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 18.2
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 2.3 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
BLU-MAXdata collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AE1

4ae1


Resolution: 2.35→29.08 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.924 / SU B: 18.3 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.385 / ESU R Free: 0.253 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25026 4932 5.1 %RANDOM
Rwork0.20722 ---
obs0.20958 91347 98.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 66.023 Å2
Baniso -1Baniso -2Baniso -3
1-1.84 Å2-1.35 Å21.23 Å2
2---1.5 Å2-2.22 Å2
3----0.66 Å2
Refinement stepCycle: 1 / Resolution: 2.35→29.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15714 0 21 351 16086
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01916069
X-RAY DIFFRACTIONr_bond_other_d0.0010.0215208
X-RAY DIFFRACTIONr_angle_refined_deg1.1741.95321771
X-RAY DIFFRACTIONr_angle_other_deg0.669335147
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.42952030
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.22225.328702
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.712152760
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.0661553
X-RAY DIFFRACTIONr_chiral_restr0.0690.22456
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.02118242
X-RAY DIFFRACTIONr_gen_planes_other0.0160.023501
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.33.7738156
X-RAY DIFFRACTIONr_mcbond_other2.2983.7738155
X-RAY DIFFRACTIONr_mcangle_it3.5045.64910174
X-RAY DIFFRACTIONr_mcangle_other3.5055.64910175
X-RAY DIFFRACTIONr_scbond_it2.6764.117913
X-RAY DIFFRACTIONr_scbond_other2.6764.117913
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2636.03111598
X-RAY DIFFRACTIONr_long_range_B_refined7.0130.58118172
X-RAY DIFFRACTIONr_long_range_B_other7.0130.5818172
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 331 -
Rwork0.272 6716 -
obs--97.74 %
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)
13.6804-2.0810.95024.4501-1.73253.3817-0.3147-0.2070.33910.38220.1396-0.1737-0.1395-0.35330.17510.08180.11490.01860.27370.09130.130617.328628.54914.6097
24.0064-0.57790.06173.2669-0.39492.206-0.1722-0.32980.74960.3630.08930.1106-0.3598-0.55130.08290.12290.1732-0.00180.3342-0.02770.250416.935936.098714.9558
31.58840.0651-0.53572.3788-0.36072.7226-0.2744-0.3174-0.47090.0775-0.0216-0.21850.65870.32120.2960.31660.18970.0670.20040.17340.298743.21973.21068.2991
42.98760.4982-0.0161.9762-0.27112.1177-0.11630.4139-0.0206-0.41780.12870.04360.1934-0.2375-0.01240.19150.0035-0.02550.15760.0470.065845.630635.4162-18.6398
53.442-1.0409-1.79862.24130.57882.10920.00120.2469-0.0557-0.0127-0.09760.2082-0.1617-0.07210.09640.22160.05-0.01320.06770.03550.074954.934860.794-20.6198
62.5435-0.2723-0.58083.3388-0.00271.840.04670.38170.1898-0.2271-0.01940.5832-0.4219-0.2502-0.02740.29990.1075-0.06270.12920.08250.226448.316962.564-20.595
72.29940.3902-0.58151.4146-0.87142.5236-0.1645-0.0141-0.4273-0.371-0.1647-0.49870.4760.49930.32920.21590.19530.12540.27050.1170.359376.429531.5763-13.9055
81.38020.0944-0.42222.79410.15932.00570.0572-0.31540.05790.3635-0.0356-0.0361-0.17050.2331-0.02160.13340.0375-0.02520.24080.06150.107944.384933.917912.9452
92.5353-0.55341.5962.81010.42633.0893-0.02640.27650.1819-0.0957-0.1113-0.37440.18210.03530.13770.23930.043-0.06390.07680.02020.137248.2922-31.0453-84.4865
102.8844-0.40110.44693.6290.11771.60850.06120.3932-0.2383-0.3239-0.0017-0.68510.38540.223-0.05950.2650.09220.01840.0936-0.0470.195354.8602-32.659-84.6385
111.96330.2953-0.14111.430.93023.0467-0.07440.09770.3948-0.4444-0.20230.5536-0.4622-0.63440.27670.23720.1856-0.23270.3129-0.01410.422625.9538-2.0891-77.993
121.39460.12830.29982.9884-0.40512.08210.0223-0.2366-0.01450.3792-0.03120.02190.1724-0.19880.00890.13740.0431-0.04090.18330.02080.098558.0115-4.0496-51.0417
134.1604-1.9438-1.21593.81121.92372.5056-0.2792-0.2858-0.32720.35780.11220.17820.1120.42470.1670.14490.1391-0.08690.38860.00090.252484.52121.0775-49.2177
143.6826-0.6372-0.2813.29820.64132.398-0.2251-0.3982-0.71280.45170.1161-0.03940.40750.64180.10910.18230.1898-0.0670.40610.09990.390985.5514-6.4399-49.1646
151.46030.25770.60082.56420.57742.8021-0.2689-0.25930.40180.0517-0.02670.2418-0.631-0.31480.29560.29120.183-0.15950.1751-0.05730.284359.203826.4553-55.7355
162.88160.5097-0.29961.89560.39672.2395-0.14370.3894-0.0054-0.4740.1602-0.093-0.25020.2385-0.01650.2414-0.0137-0.04720.14520.00650.093956.8497-5.8251-82.6784
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 69
2X-RAY DIFFRACTION2A70 - 167
3X-RAY DIFFRACTION3A168 - 379
4X-RAY DIFFRACTION4A380 - 535
5X-RAY DIFFRACTION5B3 - 70
6X-RAY DIFFRACTION6B71 - 170
7X-RAY DIFFRACTION7B171 - 379
8X-RAY DIFFRACTION8B380 - 535
9X-RAY DIFFRACTION9C1 - 69
10X-RAY DIFFRACTION10C70 - 167
11X-RAY DIFFRACTION11C168 - 379
12X-RAY DIFFRACTION12C380 - 535
13X-RAY DIFFRACTION13D1 - 70
14X-RAY DIFFRACTION14D71 - 167
15X-RAY DIFFRACTION15D168 - 381
16X-RAY DIFFRACTION16D382 - 535

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