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- PDB-4l8i: Crystal structure of RSV epitope scaffold FFL_005 -

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Basic information

Entry
Database: PDB / ID: 4l8i
TitleCrystal structure of RSV epitope scaffold FFL_005
ComponentsRSV epitope scaffold FFL_005
KeywordsIMMUNE SYSTEM / three-helix bundle
Function / homologyRibosome-recycling factor / Topoisomerase I; Chain A, domain 4 / Orthogonal Bundle / Mainly Alpha
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsJardine, J. / Correnti, C. / Holmes, M.A. / Strong, R.K. / Schief, W.R.
CitationJournal: Nature / Year: 2014
Title: Proof of principle for epitope-focused vaccine design.
Authors: Correia, B.E. / Bates, J.T. / Loomis, R.J. / Baneyx, G. / Carrico, C. / Jardine, J.G. / Rupert, P. / Correnti, C. / Kalyuzhniy, O. / Vittal, V. / Connell, M.J. / Stevens, E. / Schroeter, A. ...Authors: Correia, B.E. / Bates, J.T. / Loomis, R.J. / Baneyx, G. / Carrico, C. / Jardine, J.G. / Rupert, P. / Correnti, C. / Kalyuzhniy, O. / Vittal, V. / Connell, M.J. / Stevens, E. / Schroeter, A. / Chen, M. / Macpherson, S. / Serra, A.M. / Adachi, Y. / Holmes, M.A. / Li, Y. / Klevit, R.E. / Graham, B.S. / Wyatt, R.T. / Baker, D. / Strong, R.K. / Crowe, J.E. / Johnson, P.R. / Schief, W.R.
History
DepositionJun 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RSV epitope scaffold FFL_005
B: RSV epitope scaffold FFL_005


Theoretical massNumber of molelcules
Total (without water)27,4202
Polymers27,4202
Non-polymers00
Water2,756153
1
A: RSV epitope scaffold FFL_005


Theoretical massNumber of molelcules
Total (without water)13,7101
Polymers13,7101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RSV epitope scaffold FFL_005


Theoretical massNumber of molelcules
Total (without water)13,7101
Polymers13,7101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-7 kcal/mol
Surface area13250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.406, 53.406, 178.508
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein RSV epitope scaffold FFL_005


Mass: 13709.756 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.68 Å3/Da / Density % sol: 54.11 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 22% PEG 3350, 0.2M ammonium citrate tribasic, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 20776 / % possible obs: 99.3 % / Redundancy: 7 % / Rmerge(I) obs: 0.067 / Χ2: 1.007 / Net I/σ(I): 15.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.076.60.39219330.9194
2.07-2.157.20.25820390.981100
2.15-2.257.20.19420381.0591100
2.25-2.377.20.14320511.0251100
2.37-2.527.10.10720621.0451100
2.52-2.717.20.08420690.9961100
2.71-2.997.10.06920860.9851100
2.99-3.427.10.06220880.9681100
3.42-4.3170.08121281.093199.9
4.31-506.40.03822821.005199.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→46.25 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.115 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1064 5.1 %RANDOM
Rwork0.2068 ---
obs0.2089 20687 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 96.55 Å2 / Biso mean: 40.8097 Å2 / Biso min: 10.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å2-0 Å2
2--0.02 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2→46.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1800 0 0 153 1953
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221842
X-RAY DIFFRACTIONr_bond_other_d00.021266
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.9452481
X-RAY DIFFRACTIONr_angle_other_deg0.90433078
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7395228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15224.45792
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.60615349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.51515
X-RAY DIFFRACTIONr_chiral_restr0.0680.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022046
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02375
X-RAY DIFFRACTIONr_mcbond_it1.60721135
X-RAY DIFFRACTIONr_mcbond_other0.5382451
X-RAY DIFFRACTIONr_mcangle_it2.72331811
X-RAY DIFFRACTIONr_scbond_it4.4854707
X-RAY DIFFRACTIONr_scangle_it6.6936668
LS refinement shellResolution: 2.003→2.055 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 70 -
Rwork0.235 1433 -
all-1503 -
obs--98.36 %
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)
15.3387-3.6117-2.23365.86652.39884.0571-0.0959-0.5320.1150.24570.019-0.4196-0.03050.50660.07690.1238-0.1301-0.03120.28080.11720.1556-14.621710.264328.5882
23.1778-1.4987-1.0753.23140.52341.52960.0686-0.1353-0.0374-0.0486-0.1345-0.0985-0.08870.16830.06590.1599-0.09760.00260.21040.03660.1363-21.107614.870722.967
33.84411.5336-4.210.933-1.64924.76430.21860.1257-0.00020.0688-0.07640.0136-0.3897-0.1014-0.14230.2137-0.06750.06420.1526-0.01660.1685-22.889930.68757.4729
48.1129-1.105-7.01711.62931.26797.52680.1487-0.26010.0291-0.02260.002-0.1779-0.10020.2322-0.15070.1144-0.05710.01660.1355-0.04030.1555-28.351121.05416.2311
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 38
2X-RAY DIFFRACTION2A39 - 115
3X-RAY DIFFRACTION3B1 - 71
4X-RAY DIFFRACTION4B72 - 112

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