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- PDB-5ude: Crystal Structure of RSV F B9320 DS-Cav1 -

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Basic information

Entry
Database: PDB / ID: 5ude
TitleCrystal Structure of RSV F B9320 DS-Cav1
ComponentsFusion glycoprotein F0
KeywordsVIRAL PROTEIN / fusion glycoprotein / virus
Function / homologyPrecursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / host cell plasma membrane / virion membrane / plasma membrane / Fusion glycoprotein F0
Function and homology information
Biological speciesHuman Respiratory syncytial virus 9320
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.001 Å
AuthorsMcLellan, J.S.
CitationJournal: Sci Transl Med / Year: 2017
Title: A highly potent extended half-life antibody as a potential RSV vaccine surrogate for all infants.
Authors: Zhu, Q. / McLellan, J.S. / Kallewaard, N.L. / Ulbrandt, N.D. / Palaszynski, S. / Zhang, J. / Moldt, B. / Khan, A. / Svabek, C. / McAuliffe, J.M. / Wrapp, D. / Patel, N.K. / Cook, K.E. / ...Authors: Zhu, Q. / McLellan, J.S. / Kallewaard, N.L. / Ulbrandt, N.D. / Palaszynski, S. / Zhang, J. / Moldt, B. / Khan, A. / Svabek, C. / McAuliffe, J.M. / Wrapp, D. / Patel, N.K. / Cook, K.E. / Richter, B.W.M. / Ryan, P.C. / Yuan, A.Q. / Suzich, J.A.
History
DepositionDec 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 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

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Assembly

Deposited unit
F: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5022
Polymers63,4061
Non-polymers961
Water00
1
F: Fusion glycoprotein F0
hetero molecules

F: Fusion glycoprotein F0
hetero molecules

F: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,5076
Polymers190,2193
Non-polymers2883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area12340 Å2
ΔGint-58 kcal/mol
Surface area53300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.430, 170.430, 170.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein Fusion glycoprotein F0


Mass: 63406.281 Da / Num. of mol.: 1 / Mutation: S155C, S190F, V207L, S290C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human Respiratory syncytial virus 9320 / Plasmid: paH / Cell line (production host): 293F / Production host: Homo sapiens (human) / References: UniProt: Q6V2E7
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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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: 3.25 Å3/Da / Density % sol: 62.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% w/v PEG1500, 0.1 M Tris pH 7.5, 0.1 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3→42.61 Å / Num. obs: 17606 / % possible obs: 99.5 % / Redundancy: 5.7 % / Biso Wilson estimate: 56.962 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.209 / Rpim(I) all: 0.093 / Rrim(I) all: 0.229 / Net I/σ(I): 7.8 / Num. measured all: 99952 / Scaling rejects: 4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Diffraction-ID% possible all
3-3.215.60.97231180.6591100
8.49-42.615.10.050.997195.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOSFLMdata reduction
Aimless0.3.6data scaling
PHASERphasing
PHENIX(1.11.1_2575: ???)refinement
PDB_EXTRACT3.22data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MMS

4mms


Resolution: 3.001→42.608 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.71
RfactorNum. reflection% reflectionSelection details
Rfree0.2338 844 4.86 %Random
Rwork0.1926 ---
obs0.1946 17376 99.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 172.54 Å2 / Biso mean: 55.3035 Å2 / Biso min: 20.61 Å2
Refinement stepCycle: final / Resolution: 3.001→42.608 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3447 0 5 0 3452
Biso mean--82.43 --
Num. residues----444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063509
X-RAY DIFFRACTIONf_angle_d0.7814762
X-RAY DIFFRACTIONf_chiral_restr0.05574
X-RAY DIFFRACTIONf_plane_restr0.005595
X-RAY DIFFRACTIONf_dihedral_angle_d2.8362131
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0006-3.18860.30471570.299526942851100
3.1886-3.43470.27711410.232827042845100
3.4347-3.78010.25131340.210127432877100
3.7801-4.32670.19481390.164627322871100
4.3267-5.44940.2011260.15172787291399
5.4494-42.61180.23031470.18912872301997
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)
10.9997-0.6314-0.72265.33793.64894.1338-0.0719-0.0635-0.20940.61690.00670.33840.6767-0.21620.15040.3017-0.0097-0.00950.21830.06240.33823.4281-0.800626.0729
25.00783.3804-2.6513.5625-0.95022.0668-0.18671.18380.73150.07420.0483-0.1206-0.2264-0.04960.05790.87850.3184-0.03170.9132-0.19711.24858.1655-24.239-17.921
37.4394-1.8575-2.92250.47190.74531.175-0.1007-0.4478-0.41920.19490.1551-0.14750.2631-0.0371-0.04221.2705-0.02330.1561.84450.40161.2335-1.5784-21.7978-28.2936
46.5833-3.4791.29755.7253-2.52036.43250.31310.6457-0.2113-0.178-0.18150.0074-0.09390.4372-0.19780.5605-0.13630.07320.4172-0.15610.41434.8744-14.9246-13.3841
54.38692.30511.40431.24851.14084.9580.03970.4651-0.8628-0.4310.333-0.46820.43860.4686-0.32970.46890.1185-0.06290.35420.04750.580716.9012-16.47369.6425
63.5904-2.1526-1.00572.62520.00633.8345-0.0719-0.205-1.4789-0.0252-0.01630.23371.1310.02610.15030.8611-0.0754-0.13090.32170.06880.79066.888-26.62919.3695
71.57490.34790.94731.799-0.741.33310.10870.7092-0.7879-0.6114-0.14860.10530.6163-0.2007-0.40541.0744-0.1369-0.38490.6843-0.4580.8428-5.228-24.9005-15.5942
81.13280.27840.33262.63032.51643.2202-0.08240.0618-0.3143-0.14450.15440.26450.2765-0.1365-0.03340.3607-0.0413-0.0770.24520.01510.3933.707-10.11813.8125
92.7720.9394-0.14443.81742.66092.73320.10890.01590.0982-0.74290.0110.1455-0.0896-0.2377-0.12180.24430.0014-0.01290.30410.11040.22559.128310.705928.8199
102.8225-1.07640.96312.0794-0.60632.0783-0.0626-0.14030.21780.31460.049-0.1767-0.11870.09210.01270.30790.0210.01250.2536-0.05670.26335.81223.125533.4757
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'F' and (resid 26 through 62 )F26 - 62
2X-RAY DIFFRACTION2chain 'F' and (resid 63 through 67 )F63 - 67
3X-RAY DIFFRACTION3chain 'F' and (resid 68 through 73 )F68 - 73
4X-RAY DIFFRACTION4chain 'F' and (resid 74 through 99 )F74 - 99
5X-RAY DIFFRACTION5chain 'F' and (resid 138 through 171 )F138 - 171
6X-RAY DIFFRACTION6chain 'F' and (resid 172 through 194 )F172 - 194
7X-RAY DIFFRACTION7chain 'F' and (resid 195 through 227 )F195 - 227
8X-RAY DIFFRACTION8chain 'F' and (resid 228 through 321 )F228 - 321
9X-RAY DIFFRACTION9chain 'F' and (resid 322 through 376 )F322 - 376
10X-RAY DIFFRACTION10chain 'F' and (resid 377 through 506 )F377 - 506

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