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- PDB-3rhu: Epitope backbone grafting by computational design for improved pr... -

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Basic information

Entry
Database: PDB / ID: 3rhu
TitleEpitope backbone grafting by computational design for improved presentation of linear epitopes on scaffold proteins
ComponentsSC_1wnu
KeywordsDE NOVO PROTEIN / protein grafting / flexible backbone design / epitope-scaffold / HIV / immunogen design
Function / homology
Function and homology information


Ser-tRNA(Ala) hydrolase activity / aminoacyl-tRNA editing activity / nucleotide binding / metal ion binding / cytoplasm
Similarity search - Function
Replication Terminator Protein; Chain A, domain 2 - #20 / Threonyl-trna Synthetase; Chain A, domain 2 / Replication Terminator Protein; Chain A, domain 2 / Threonyl-tRNA Synthetase; Chain A, domain 2 / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Alanyl-tRNA editing protein AlaX-S
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsAzoitei, M.L. / Ban, Y.A. / Julien, J.P. / Bryson, S. / Schroeter, A. / Kalyuzhniy, O. / Porter, J.R. / Adachi, Y. / Baker, D. / Szabo, E. ...Azoitei, M.L. / Ban, Y.A. / Julien, J.P. / Bryson, S. / Schroeter, A. / Kalyuzhniy, O. / Porter, J.R. / Adachi, Y. / Baker, D. / Szabo, E. / Pai, E.F. / Schief, W.R.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Computational design of high-affinity epitope scaffolds by backbone grafting of a linear epitope.
Authors: Azoitei, M.L. / Ban, Y.E. / Julien, J.P. / Bryson, S. / Schroeter, A. / Kalyuzhniy, O. / Porter, J.R. / Adachi, Y. / Baker, D. / Pai, E.F. / Schief, W.R.
History
DepositionApr 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2011Group: Database references
Revision 1.2Jan 18, 2012Group: Database references
Revision 1.3Jul 26, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_detector / entity_src_gen / software / Item: _diffrn_detector.detector
Revision 1.4Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SC_1wnu
B: SC_1wnu


Theoretical massNumber of molelcules
Total (without water)36,3722
Polymers36,3722
Non-polymers00
Water00
1
A: SC_1wnu


Theoretical massNumber of molelcules
Total (without water)18,1861
Polymers18,1861
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SC_1wnu


Theoretical massNumber of molelcules
Total (without water)18,1861
Polymers18,1861
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-12 kcal/mol
Surface area13900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.650, 103.650, 85.669
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein SC_1wnu


Mass: 18185.982 Da / Num. of mol.: 2 / Fragment: SEE REMARK 999 / Mutation: UNP M1S,V22T,L23A,E26D,Y31T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: alaXS, PH0574 / Production host: Escherichia coli (E. coli) / References: UniProt: O58307
Sequence detailsPROTEIN CONSTRUCT CONSISTS OF UNP RESIDUES 1-154 WITH A C-TERMINAL EXPRESSION TAG AND UNP RESIDUES ...PROTEIN CONSTRUCT CONSISTS OF UNP RESIDUES 1-154 WITH A C-TERMINAL EXPRESSION TAG AND UNP RESIDUES 46-60 (FDRKPSDEEIREIER) REPLACED BY EPITOPE AALEPDKWGIAAIEA

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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: 3.16 Å3/Da / Density % sol: 61.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2.8 M sodium chloride, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 1, 2011
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.8→73.3 Å / Num. all: 11406 / Num. obs: 11260 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.064 / Net I/σ(I): 26.7
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 5.2 / Rsym value: 0.365 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WNU

1wnu


Resolution: 2.8→73.3 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.879 / SU B: 22.695 / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.887 / ESU R Free: 0.405 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.31223 538 4.8 %RANDOM
Rwork0.28027 ---
obs0.28182 10722 99.83 %-
all-10740 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 73.692 Å2
Baniso -1Baniso -2Baniso -3
1-3.27 Å20 Å20 Å2
2--3.27 Å20 Å2
3----6.53 Å2
Refinement stepCycle: LAST / Resolution: 2.8→73.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2228 0 0 0 2228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222268
X-RAY DIFFRACTIONr_angle_refined_deg1.1091.9643056
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7865278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.76224.66790
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.65915440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9521510
X-RAY DIFFRACTIONr_chiral_restr0.0750.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211624
X-RAY DIFFRACTIONr_mcbond_it0.4671.51398
X-RAY DIFFRACTIONr_mcangle_it0.86422260
X-RAY DIFFRACTIONr_scbond_it0.7233870
X-RAY DIFFRACTIONr_scangle_it1.3734.5796
LS refinement shellResolution: 2.798→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 46 -
Rwork0.326 771 -
obs--98.91 %

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