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- PDB-4eq3: Crystal Structure Analysis of Selenomethionine (Se-Met) Substitut... -

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Basic information

Entry
Database: PDB / ID: 4eq3
TitleCrystal Structure Analysis of Selenomethionine (Se-Met) Substituted 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
Interferon gamma receptor 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.001 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

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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)24,8331
Polymers24,8331
Non-polymers00
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.608, 63.608, 215.750
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: 24833.285 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.: 221 / 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: 2.54 Å3/Da / Density % sol: 51.51 %
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: 0.97923, 0.9789, 0.9791, 0.9000
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 12, 2011
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979231
20.97891
30.97911
40.91
ReflectionResolution: 2→50 Å / Num. all: 17153 / Num. obs: 17153 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 32.6 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 59.328
Reflection shellResolution: 2→2.07 Å / Redundancy: 35.8 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 18.095 / Num. unique all: 875 / Rsym value: 0.302 / % possible all: 97.1

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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: MAD / Resolution: 2.001→38.539 Å / SU ML: 0.2 / σ(F): 0.22 / Phase error: 23.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2602 875 5.1 %RANDOM
Rwork0.2334 ---
all0.2347 17153 --
obs0.2347 16638 93.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.155 Å2 / ksol: 0.352 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.4852 Å2-0 Å2-0 Å2
2--4.4852 Å20 Å2
3----8.9705 Å2
Refinement stepCycle: LAST / Resolution: 2.001→38.539 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1643 0 0 221 1864
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141692
X-RAY DIFFRACTIONf_angle_d1.2882299
X-RAY DIFFRACTIONf_dihedral_angle_d21.332603
X-RAY DIFFRACTIONf_chiral_restr0.098251
X-RAY DIFFRACTIONf_plane_restr0.006295
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0012-2.12660.27411320.2421254890
2.1266-2.29070.28361310.2609246788
2.2907-2.52120.2381440.2559267294
2.5212-2.88590.29091540.2574276196
2.8859-3.63550.28841460.2228284797
3.6355-38.54640.22751680.2118298395
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)
10.7216-0.17250.15161.0024-0.24991.541-0.0081-0.00360.0932-0.139-0.08640.0758-0.218-0.12450.08850.2330.0791-0.06640.1985-0.04220.2039-34.451922.11997.0915
20.80870.10630.93231.3465-0.68691.50760.0508-0.0563-0.0933-0.0213-0.1275-0.15990.1452-0.10070.06330.2225-0.01230.00270.18440.02210.1985-23.5404-7.41220.7416
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resseq 2:101)
2X-RAY DIFFRACTION2chain A and (resseq 102:207)

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