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- PDB-5kux: Designed influenza hemagglutinin binding protein HSB.2 -

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Basic information

Entry
Database: PDB / ID: 5kux
TitleDesigned influenza hemagglutinin binding protein HSB.2
ComponentsDesigned influenza inhibitor protein HSB.2
KeywordsPROTEIN BINDING / Influenza / inhibitor / designed protein / cystatin
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLee, P.S. / Bernard, S.M. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R56 AI117675 United States
CitationJournal: Nat. Biotechnol. / Year: 2017
Title: Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site.
Authors: Strauch, E.M. / Bernard, S.M. / La, D. / Bohn, A.J. / Lee, P.S. / Anderson, C.E. / Nieusma, T. / Holstein, C.A. / Garcia, N.K. / Hooper, K.A. / Ravichandran, R. / Nelson, J.W. / Sheffler, W. ...Authors: Strauch, E.M. / Bernard, S.M. / La, D. / Bohn, A.J. / Lee, P.S. / Anderson, C.E. / Nieusma, T. / Holstein, C.A. / Garcia, N.K. / Hooper, K.A. / Ravichandran, R. / Nelson, J.W. / Sheffler, W. / Bloom, J.D. / Lee, K.K. / Ward, A.B. / Yager, P. / Fuller, D.H. / Wilson, I.A. / Baker, D.
History
DepositionJul 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 26, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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: Designed influenza inhibitor protein HSB.2


Theoretical massNumber of molelcules
Total (without water)11,0171
Polymers11,0171
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Designed influenza inhibitor protein HSB.2

A: Designed influenza inhibitor protein HSB.2


Theoretical massNumber of molelcules
Total (without water)22,0352
Polymers22,0352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Buried area4140 Å2
ΔGint-35 kcal/mol
Surface area10450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.385, 58.385, 69.449
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Designed influenza inhibitor protein HSB.2


Mass: 11017.269 Da / Num. of mol.: 1
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


Mass: 18.015 Da / Num. of mol.: 14 / 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: 3.1 Å3/Da / Density % sol: 60.34 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / Details: 15% PEG 8000, 0.1 M HEPES pH 7.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 12579 / % possible obs: 97.1 % / Redundancy: 7.9 % / Net I/σ(I): 25.9
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.965 / % possible all: 80.7

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W9P

2w9p


Resolution: 1.8→40.877 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 38.75
RfactorNum. reflection% reflection
Rfree0.2361 585 4.65 %
Rwork0.1963 --
obs0.1981 12575 95.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→40.877 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms718 0 0 14 732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009739
X-RAY DIFFRACTIONf_angle_d0.9551005
X-RAY DIFFRACTIONf_dihedral_angle_d17.855429
X-RAY DIFFRACTIONf_chiral_restr0.067112
X-RAY DIFFRACTIONf_plane_restr0.005130
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8005-1.98170.42561300.32662617X-RAY DIFFRACTION85
1.9817-2.26840.29121480.24593050X-RAY DIFFRACTION99
2.2684-2.85780.30681500.2533086X-RAY DIFFRACTION100
2.8578-40.88730.20361570.16873237X-RAY DIFFRACTION100
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)
17.2084-3.36292.48582.0936-0.23376.06220.1879-0.13830.91020.94680.3821-1.1953-0.50080.9533-0.46080.6393-0.1099-0.10080.7421-0.13440.685-16.119515.9171-16.2283
27.6974-2.10940.67088.19112.46214.01510.20920.57680.1841-0.1112-0.30950.0113-0.8875-0.42690.10980.5153-0.0520.02190.57650.07470.2748-30.96317.965-22.7595
32.89442.85881.68698.57793.07363.29340.0259-0.3850.0797-0.2103-0.2791-0.29630.0415-0.10220.28540.33890.0684-0.02470.60460.04660.3835-23.7976-7.1828-23.8903
44.15830.79563.70561.43561.95714.6846-0.1715-0.16130.0772-0.4142-0.14360.36780.3031-0.61310.14060.4237-0.0420.01350.56490.00080.2945-31.0747-15.8962-30.8592
52.71512.52792.9882.64832.90793.5209-0.023-0.9701-0.15331.162-0.3285-0.48140.4820.85590.34010.46430.0295-0.05430.65450.050.5508-19.935-6.1687-16.33
63.9343-2.03361.7963.22041.63436.4175-0.2827-0.27380.2213-1.1279-0.53340.8156-0.7291-1.10630.62040.48160.0097-0.00370.58570.00390.3308-33.6624-15.2925-32.4318
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 4:16)
2X-RAY DIFFRACTION2(chain A and resid 17:42)
3X-RAY DIFFRACTION3(chain A and resid 43:64)
4X-RAY DIFFRACTION4(chain A and resid 65:74)
5X-RAY DIFFRACTION5(chain A and resid 75:82)
6X-RAY DIFFRACTION6(chain A and resid 83:95)

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