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

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Basic information

Entry
Database: PDB / ID: 3rfn
TitleEpitope backbone grafting by computational design for improved presentation of linear epitopes on scaffold proteins
ComponentsBB_1wnu_001
KeywordsDE NOVO PROTEIN / protein grafting / flexible backbone design / epitope-scaffold / HIV / immunogen design
Function / homology
Function and homology information


aminoacyl-tRNA ligase activity / tRNA aminoacylation / aminoacyl-tRNA deacylase activity / ATP 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, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / 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 / MIR / Resolution: 1.8 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 6, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: BB_1wnu_001
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2112
Polymers18,1461
Non-polymers651
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.8, 36.1, 46.3
Angle α, β, γ (deg.)90.0, 99.4, 90.0
Int Tables number5
Space group name H-MC121

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Components

#1: Protein BB_1wnu_001


Mass: 18146.027 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Mutation: UNP V22A,L23A,E26A,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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPROTEIN CONSTRUCT CONSISTS OF UNP RESIDUES 2-154 WITH A C-TERMINAL EXPRESSION TAG AND UNP RESIDUES ...PROTEIN CONSTRUCT CONSISTS OF UNP RESIDUES 2-154 WITH A C-TERMINAL EXPRESSION TAG AND UNP RESIDUES 46-60 (FDRKPSDEEIREIER) REPLACED BY EPITOPE AALELDKWAWAAMEA

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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: 2.12 Å3/Da / Density % sol: 42.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2.8 M NaCl, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 93.2 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 3, 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: 1.8→17 Å / Num. all: 15677 / Num. obs: 15316 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.75 % / Rsym value: 0.022 / Net I/σ(I): 25
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 1.44 % / Mean I/σ(I) obs: 5.9 / Rsym value: 0.132 / % possible all: 89

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 1WNU

1wnu


Resolution: 1.8→17 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.237 691 -RANDOM
Rwork0.219 ---
all0.219 14334 --
obs0.219 13181 96.8 %-
Refinement stepCycle: LAST / Resolution: 1.8→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1201 0 1 88 1290
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0069
X-RAY DIFFRACTIONc_angle_deg1.6

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