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- PDB-1fnl: CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF A HUMAN FCGRIII -

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Basic information

Entry
Database: PDB / ID: 1fnl
TitleCRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF A HUMAN FCGRIII
ComponentsLOW AFFINITY IMMUNOGLOBULIN GAMMA FC REGION RECEPTOR III-B
KeywordsIMMUNE SYSTEM RECEPTOR / BETA SANDWICH / IMMUNOGLOBULIN-LIKE / RECEPTOR
Function / homology
Function and homology information


GPI anchor binding / Post-translational modification: synthesis of GPI-anchored proteins / IgG binding / regulation of immune response / side of membrane / secretory granule membrane / transmembrane signaling receptor activity / cell surface receptor signaling pathway / immune response / Neutrophil degranulation ...GPI anchor binding / Post-translational modification: synthesis of GPI-anchored proteins / IgG binding / regulation of immune response / side of membrane / secretory granule membrane / transmembrane signaling receptor activity / cell surface receptor signaling pathway / immune response / Neutrophil degranulation / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Low affinity immunoglobulin gamma Fc region receptor III-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsZhang, Y. / Boesen, C.C. / Radaev, S. / Brooks, A.G. / Fridman, W.H. / Sautes-Fridman, C. / Sun, P.D.
CitationJournal: Immunity / Year: 2000
Title: Crystal structure of the extracellular domain of a human Fc gamma RIII.
Authors: Zhang, Y. / Boesen, C.C. / Radaev, S. / Brooks, A.G. / Fridman, W.H. / Sautes-Fridman, C. / Sun, P.D.
History
DepositionAug 22, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LOW AFFINITY IMMUNOGLOBULIN GAMMA FC REGION RECEPTOR III-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4053
Polymers20,0041
Non-polymers4012
Water4,053225
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.427, 85.733, 36.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a monomer

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Components

#1: Protein LOW AFFINITY IMMUNOGLOBULIN GAMMA FC REGION RECEPTOR III-B


Mass: 20004.285 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR LIGAND BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET30 / Production host: Escherichia coli (E. coli) / References: UniProt: O75015
#2: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.62 Å3/Da / Density % sol: 53.12 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 6.5
Details: PEG 8000, Sodium Hepes, pH 6.5, EVAPORATION, temperature 298.0K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 %PEG80001reservoir
250 mMsodium HEPES1reservoir
350 mMTris1drop
450 mM1dropNaCl
50.010 mMprotain1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 10, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 36093 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 29.5
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2 % / Rmerge(I) obs: 0.21 / Num. unique all: 3033 / % possible all: 80.1
Reflection
*PLUS
Num. obs: 36180
Reflection shell
*PLUS
% possible obs: 80.1 % / Mean I/σ(I) obs: 6.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementResolution: 1.8→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.216 3475 -RANDOM
Rwork0.184 ---
obs-36093 95.8 %-
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1388 0 2 225 1615
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.36
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 24.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.73
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.6

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