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

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Basic information

Entry
Database: PDB / ID: 3rij
TitleEpitope backbone grafting by computational design for improved presentation of linear epitopes on scaffold proteins
ComponentsSC_2cx5
KeywordsDE NOVO PROTEIN / protein grafting / flexible backbone design / epitope-scaffold / HIV / immunogen design
Function / homologyYbaK protein / YbaK/aminoacyl-tRNA synthetase-associated domain / YbaK/aminoacyl-tRNA synthetase-associated domain / Aminoacyl-tRNA editing domain / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / aminoacyl-tRNA deacylase activity / Alpha-Beta Complex / Alpha Beta / YbaK/aminoacyl-tRNA synthetase-associated domain-containing protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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 13, 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: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SC_2cx5
B: SC_2cx5
C: SC_2cx5
D: SC_2cx5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4875
Polymers69,3954
Non-polymers921
Water8,089449
1
A: SC_2cx5


Theoretical massNumber of molelcules
Total (without water)17,3491
Polymers17,3491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SC_2cx5


Theoretical massNumber of molelcules
Total (without water)17,3491
Polymers17,3491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: SC_2cx5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4412
Polymers17,3491
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: SC_2cx5


Theoretical massNumber of molelcules
Total (without water)17,3491
Polymers17,3491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.0, 70.0, 131.4
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
SC_2cx5


Mass: 17348.719 Da / Num. of mol.: 4 / Fragment: SEE REMARK 999 / Mutation: UNP F54Y,V55G,D99A,I100A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: TTHA1699 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SHN1
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 449 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPROTEIN CONSTRUCT CONSISTS OF UNP RESIDUES 2-158 WITH A C-TERMINAL EXPRESSION TAG AND UNP RESIDUES ...PROTEIN CONSTRUCT CONSISTS OF UNP RESIDUES 2-158 WITH A C-TERMINAL EXPRESSION TAG AND UNP RESIDUES 85-94 (RQATPEEVRE) REPLACED BY EPITOPE LEADKWAVAA

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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: 2.32 Å3/Da / Density % sol: 46.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.0 M ammonium sulfate, 4% PEG400, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 1, 2010
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→17 Å / Num. all: 28092 / Num. obs: 27812 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.069 / Net I/σ(I): 19
Reflection shellResolution: 2.3→2.4 Å / Mean I/σ(I) obs: 5.4 / Rsym value: 0.38 / % possible all: 97.9

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Processing

Software
NameClassification
MAR345dtbdata collection
PHASERphasing
CNSrefinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CX5

2cx5


Resolution: 2.3→17 Å / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2938 1385 4.9 %RANDOM
Rwork0.2523 26144 --
all-27993 --
obs-26144 98.3 %-
Solvent computationBsol: 95.6017 Å2
Displacement parametersBiso max: 61.47 Å2 / Biso mean: 29.2322 Å2 / Biso min: 2.69 Å2
Baniso -1Baniso -2Baniso -3
1--4.621 Å20 Å20 Å2
2---4.621 Å20 Å2
3---9.243 Å2
Refinement stepCycle: LAST / Resolution: 2.3→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4536 0 6 449 4991
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3591.5
X-RAY DIFFRACTIONc_scbond_it1.8532
X-RAY DIFFRACTIONc_mcangle_it2.1662
X-RAY DIFFRACTIONc_scangle_it2.6522.5
LS refinement shellResolution: 2.3→2.33 Å /
Rfactor% reflection
Rfree0.341 5 %
Rwork0.314 -
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water.param
X-RAY DIFFRACTION3gol.param

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