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- PDB-3wvt: Structural and biochemical study of equine lentivirus receptor 1 -

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Basic information

Entry
Database: PDB / ID: 3wvt
TitleStructural and biochemical study of equine lentivirus receptor 1
ComponentsELR1
KeywordsPROTEIN BINDING / tumor necrosis factor receptor / cysteine rich domain
Function / homology
Function and homology information


membrane => GO:0016020
Similarity search - Function
Tumour necrosis factor receptor 14 / Tumor necrosis factor receptor 14/UL144, N-terminal / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Ribbon / Mainly Beta
Similarity search - Domain/homology
Uncharacterized protein / ELR1
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 Å
AuthorsQian, L.
CitationJournal: Protein Sci. / Year: 2015
Title: Structural insight into equine lentivirus receptor 1
Authors: Qian, L. / Han, X.D. / Liu, X.Q.
History
DepositionJun 7, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ELR1


Theoretical massNumber of molelcules
Total (without water)20,7221
Polymers20,7221
Non-polymers00
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.139, 81.139, 42.274
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein ELR1 / equine lentivirus receptor 1


Mass: 20722.084 Da / Num. of mol.: 1 / Fragment: UNP residues 38-206
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Cell line (production host): Schneider 2 cells / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q4G265, UniProt: F6T8I7*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 1.68 Å3/Da / Density % sol: 26.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 0.1M Citric acid, 25%(w/v) PEG3350, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 2, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 19085 / % possible obs: 86 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.5→1.6 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNSrefinement
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FHQ

4fhq


Resolution: 1.601→37.491 Å / FOM work R set: 0.8597 / SU ML: 0.12 / σ(F): 1.34 / Phase error: 20.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2003 979 5.13 %RANDOM
Rwork0.1949 ---
all0.2003 19145 --
obs0.1952 19082 99.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.31 Å2 / Biso mean: 25.45 Å2 / Biso min: 10.66 Å2
Refinement stepCycle: LAST / Resolution: 1.601→37.491 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms754 0 0 155 909
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006786
X-RAY DIFFRACTIONf_angle_d1.2431042
X-RAY DIFFRACTIONf_chiral_restr0.082112
X-RAY DIFFRACTIONf_plane_restr0.004142
X-RAY DIFFRACTIONf_dihedral_angle_d14.524295
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6012-1.68570.23861390.20472517265699
1.6857-1.79130.23881380.20625402678100
1.7913-1.92960.25041330.198525642697100
1.9296-2.12370.20211470.192725592706100
2.1237-2.4310.251600.19325502710100
2.431-3.06260.17581350.199326272762100
3.0626-37.5010.16891270.19052746287399

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