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- PDB-6rpy: Cytokine receptor-like factor 3 C-terminus residues 174-442: Hg-S... -

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Basic information

Entry
Database: PDB / ID: 6rpy
TitleCytokine receptor-like factor 3 C-terminus residues 174-442: Hg-SAD derivative
ComponentsCytokine receptor-like factor 3
KeywordsBLOOD CLOTTING / platelet development / fibronectin domain / SPRY domain
Function / homology
Function and homology information


negative regulation of G1/S transition of mitotic cell cycle / positive regulation of receptor signaling pathway via JAK-STAT / negative regulation of cell growth / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
: / Cytokine receptor-like factor 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.97 Å
AuthorsMifsud, R.W. / Yan, Y. / Bennett, C. / Read, R.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust209407/Z/17/Z United Kingdom
CitationJournal: Blood / Year: 2022
Title: CRLF3 plays a key role in the final stage of platelet genesis and is a potential therapeutic target for thrombocythemia.
Authors: Bennett, C. / Lawrence, M. / Guerrero, J.A. / Stritt, S. / Waller, A.K. / Yan, Y. / Mifsud, R.W. / Ballester-Beltran, J. / Baig, A. / Mueller, A. / Mayer, L. / Warland, J. / Penkett, C.J. / ...Authors: Bennett, C. / Lawrence, M. / Guerrero, J.A. / Stritt, S. / Waller, A.K. / Yan, Y. / Mifsud, R.W. / Ballester-Beltran, J. / Baig, A. / Mueller, A. / Mayer, L. / Warland, J. / Penkett, C.J. / Akbari, P. / Moreau, T. / Evans, A.L. / Mookerjee, S. / Hoffman, G.J. / Saeb-Parsy, K. / Adams, D.J. / Couzens, A.L. / Bender, M. / Erber, W.N. / Nieswandt, B. / Read, R.J. / Ghevaert, C.
History
DepositionMay 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytokine receptor-like factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,26412
Polymers30,0571
Non-polymers2,20611
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-199 kcal/mol
Surface area12640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.254, 40.944, 76.288
Angle α, β, γ (deg.)90.000, 98.735, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Components on special symmetry positions
IDModelComponents
11A-685-

HOH

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Components

#1: Protein Cytokine receptor-like factor 3 / Cytokine receptor-like molecule 9 / CREME-9 / Cytokine receptor-related factor 4


Mass: 30057.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-terminal domain of murine CRLF3 / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Crlf3, Creme9, Cytor4 / Production host: Escherichia coli (E. coli) / Variant (production host): BL21-CodonPlusTM-(DE3)-RP / References: UniProt: Q9Z2L7
#2: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.24 Å3/Da / Density % sol: 45.1 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20 % PEG 3,350, 0.2 M sodium formate, soaked for 16 hours with 10 mM thimerosal, cryo-protected in 25 % ethylene glycol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.006 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.006 Å / Relative weight: 1
ReflectionResolution: 1.967→27.31 Å / Num. obs: 19156 / % possible obs: 99.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 30.27 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.079 / Net I/σ(I): 16.6
Reflection shellResolution: 1.967→2.02 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.714 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1351 / CC1/2: 0.829 / Rrim(I) all: 0.845 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
xia2data reduction
xia2data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.97→27.31 Å / SU ML: 0.2502 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.2475
RfactorNum. reflection% reflectionSelection details
Rfree0.2342 907 4.74 %Random selection
Rwork0.1865 ---
obs0.1887 19150 99.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 39.61 Å2
Refinement stepCycle: LAST / Resolution: 1.97→27.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1937 0 11 93 2041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01181999
X-RAY DIFFRACTIONf_angle_d1.13432720
X-RAY DIFFRACTIONf_chiral_restr0.0652297
X-RAY DIFFRACTIONf_plane_restr0.0079356
X-RAY DIFFRACTIONf_dihedral_angle_d8.31881613
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.090.33541560.24772950X-RAY DIFFRACTION98.1
2.09-2.250.28281390.21563030X-RAY DIFFRACTION100
2.25-2.480.30151420.1963042X-RAY DIFFRACTION99.97
2.48-2.840.23541720.19573023X-RAY DIFFRACTION100
2.84-3.570.23011440.18623058X-RAY DIFFRACTION99.97
3.57-27.310.19921540.16693141X-RAY DIFFRACTION99.94

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