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- PDB-4r61: Crystal structure of a rationally designed single-chain protein m... -

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Basic information

Entry
Database: PDB / ID: 4r61
TitleCrystal structure of a rationally designed single-chain protein mimicking a trimeric gp41 N-terminal heptad-repeat region
Componentsgp41-based construct covNHR3-ABC
KeywordsVIRAL PROTEIN / coiled-coil
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsCamara-Artigas, A. / Conejero-Lara, F. / Crespillo, S. / Casares, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Single-chain protein mimetics of the N-terminal heptad-repeat region of gp41 with potential as anti-HIV-1 drugs.
Authors: Crespillo, S. / Camara-Artigas, A. / Casares, S. / Morel, B. / Cobos, E.S. / Mateo, P.L. / Mouz, N. / Martin, C.E. / Roger, M.G. / El Habib, R. / Su, B. / Moog, C. / Conejero-Lara, F.
History
DepositionAug 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Jan 14, 2015Group: Database references
Revision 1.3Sep 20, 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
A: gp41-based construct covNHR3-ABC


Theoretical massNumber of molelcules
Total (without water)20,2651
Polymers20,2651
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.956, 57.956, 257.671
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein gp41-based construct covNHR3-ABC


Mass: 20265.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli (E. coli)

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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: 2.05 Å3/Da / Density % sol: 40.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 2 M sodium chloride, 0.1 M sodium acetate trihydrate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID2910.96869
SYNCHROTRONALBA XALOC20.97926
Detector
TypeIDDetectorDateDetails
DECTRIS PILATUS 6M1PIXELFeb 10, 2014cylindrical grazing incidence mirror
DECTRIS PILATUS 6M2PIXELOct 24, 2013KB focusing mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1liquid nitrogen-cooled channel-cut Si(111)SINGLE WAVELENGTHMx-ray1
2channel-cut Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.968691
20.979261
ReflectionRedundancy: 8.6 % / Number: 28217 / Rmerge(I) obs: 0.09 / D res high: 3.1 Å / D res low: 19.8 Å / Num. obs: 3278 / % possible obs: 99.6 / Rejects: 634
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRedundancy
3.13.3110.3278
8.7719.810.0249.1
ReflectionResolution: 3.1→19.8 Å / Num. all: 5202 / Num. obs: 3278 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Biso Wilson estimate: 44.52 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 130.8 / Scaling rejects: 634
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
3.1-3.3180.32741.94637582100
8.77-19.89.10.024357.2143015891.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
Aimless0.2.17data scaling
PHASERphasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.15data extraction
BsxCuBEdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XRA

2xra


Resolution: 3.1→17.803 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.91 / σ(I): 0 / Phase error: 30.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2893 314 5.54 %RANDOM
Rwork0.2469 ---
all0.2495 ---
obs-3211 96.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 198.97 Å2 / Biso mean: 72.45 Å2 / Biso min: 12.99 Å2
Refinement stepCycle: LAST / Resolution: 3.1→17.803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1141 0 0 0 1141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051147
X-RAY DIFFRACTIONf_angle_d0.5861538
X-RAY DIFFRACTIONf_chiral_restr0.027179
X-RAY DIFFRACTIONf_plane_restr0.002201
X-RAY DIFFRACTIONf_dihedral_angle_d14.109456
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.8990.31171520.29222642279495
3.899-17.80290.2731620.21652712287498

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