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- PDB-4eq2: Crystal Structure Analysis of Chicken Interferon Gamma Receptor A... -

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Basic information

Entry
Database: PDB / ID: 4eq2
TitleCrystal Structure Analysis of Chicken Interferon Gamma Receptor Alpha Chain
ComponentsInterferon gamma receptor 1
KeywordsIMMUNE SYSTEM / INTERFERON GAMMA / BETA CHAIN / IG-LIKE STRUCTURE / LIGAND-BINDING
Function / homology
Function and homology information


cytokine receptor activity / cytokine binding / membrane
Similarity search - Function
Interferon gamma receptor alpha subunit / Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / : / Tissue factor / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like ...Interferon gamma receptor alpha subunit / Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / : / Tissue factor / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Interferon gamma receptor 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.502 Å
AuthorsPing, Z. / Qi, J. / Lu, G. / Shi, Y. / Wang, X. / Gao, G.F. / Wang, M.
CitationJournal: J.Interferon Cytokine Res. / Year: 2014
Title: Crystal structure of the interferon gamma receptor alpha chain from chicken reveals an undetected extra helix compared with the human counterparts.
Authors: Ping, Z. / Qi, J. / Sun, Y. / Lu, G. / Shi, Y. / Wang, X. / Gao, G.F. / Wang, M.
History
DepositionApr 18, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2May 21, 2014Group: Database references
Revision 1.3Nov 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: Interferon gamma receptor 1


Theoretical massNumber of molelcules
Total (without water)24,6461
Polymers24,6461
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.536, 63.536, 216.323
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Interferon gamma receptor 1


Mass: 24645.705 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 25-237
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B4XN22
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.56 Å3/Da / Density % sol: 51.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% (v/v) polyethylene glycol 5000 monomethyl ether, 0.1M HEPES, 0.5M sodium carbonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 15, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 9716 / Num. obs: 9650 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 23.6 % / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 35.373
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 16 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 4.685 / Num. unique all: 858 / Rsym value: 0.396 / % possible all: 93.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EQ3

4eq3


Resolution: 2.502→38.57 Å / SU ML: 0.41 / σ(F): 0.1 / Phase error: 28.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2664 426 4.71 %RANDOM
Rwork0.218 ---
all0.2203 9050 --
obs0.2203 9050 93.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.736 Å2 / ksol: 0.344 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-11.265 Å2-0 Å2-0 Å2
2--11.265 Å20 Å2
3----22.53 Å2
Refinement stepCycle: LAST / Resolution: 2.502→38.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1643 0 0 23 1666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041692
X-RAY DIFFRACTIONf_angle_d0.8112299
X-RAY DIFFRACTIONf_dihedral_angle_d17.898603
X-RAY DIFFRACTIONf_chiral_restr0.058251
X-RAY DIFFRACTIONf_plane_restr0.003295
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5021-2.590.38291270.2761258087
2.59-3.6080.25891330.2298286595
3.608-38.57450.23151660.1912317999
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)
10.4127-0.60360.03981.30110.90492.0443-0.0132-0.1361-0.14040.1397-0.130.06820.26950.2753-00.25980.09090.0550.25480.08240.31735.081-24.36819.1726
2-0.0139-0.01590.02370.50770.431.1677-0.037-0.1175-0.0287-0.22340.07550.2031-0.10580.3744-00.35730.12870.02790.30320.04570.298933.1771-18.07874.9824
30.32950.1427-0.00010.0617-0.01250.13920.0348-0.5746-0.0383-0.03160.26890.06810.06570.3386-00.49350.0184-0.00360.4009-0.01290.407223.347810.726428.889
40.32430.0799-0.17420.43120.19250.5885-0.16260.3246-0.03010.0736-0.04860.0788-0.2428-0.037300.46570.01020.00620.39960.05280.430926.00415.017816.7964
50.74750.3854-0.08951.06021.04351.35670.07680.1450.0243-0.1188-0.08710.1217-0.19710.034100.40820.00250.02820.33260.0430.35520.44378.891121.9008
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 2:60)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 61:104)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 105:120)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 121:160)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 161:207)

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