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- PDB-2icc: Extracellular Domain of CRIg -

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Basic information

Entry
Database: PDB / ID: 2icc
TitleExtracellular Domain of CRIg
ComponentsV-set and immunoglobulin domain-containing protein 4
KeywordsIMMUNE SYSTEM / Alternative Pathway / Complement Receptor / Ig like domain
Function / homology
Function and homology information


negative regulation of complement activation, alternative pathway / negative regulation of macrophage activation / complement component C3b binding / complement activation, alternative pathway / negative regulation of interleukin-2 production / negative regulation of T cell proliferation / protein-containing complex / membrane
Similarity search - Function
VSIG4, immunoglobulin variable (IgV)-like domain / V-set and immunoglobulin domain-containing protein 4 / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin ...VSIG4, immunoglobulin variable (IgV)-like domain / V-set and immunoglobulin domain-containing protein 4 / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set 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
V-set and immunoglobulin domain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsWiesmann, C.
CitationJournal: Nature / Year: 2006
Title: Structure of C3b in complex with CRIg gives insights into regulation of complement activation.
Authors: Wiesmann, C. / Katschke, K.J. / Yin, J. / Helmy, K.Y. / Steffek, M. / Fairbrother, W.J. / McCallum, S.A. / Embuscado, L. / DeForge, L. / Hass, P.E. / van Lookeren Campagne, M.
History
DepositionSep 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2006Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: V-set and immunoglobulin domain-containing protein 4


Theoretical massNumber of molelcules
Total (without water)13,5011
Polymers13,5011
Non-polymers00
Water3,477193
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.257, 50.757, 61.965
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein V-set and immunoglobulin domain-containing protein 4 / Protein Z39Ig


Mass: 13501.173 Da / Num. of mol.: 1 / Fragment: extracellular domain of CRIG
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VSIG4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y279
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 1.761057 Å3/Da / Density % sol: 30.1556 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 6.4 / Details: pH 6.4, EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. all: 39631 / Num. obs: 36270 / % possible obs: 91.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.031 / Χ2: 0.965 / Net I/σ(I): 18.7
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.219 / Num. unique all: 1949 / Χ2: 1.264 / % possible all: 50.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: murine CRIg

Resolution: 1.2→39.25 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.067 / SU ML: 0.022 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.172 1511 5 %RANDOM
Rwork0.134 ---
all0.135 30901 --
obs0.135 30315 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 9.778 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20 Å20 Å2
2---0.69 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.2→39.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms950 0 0 193 1143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022973
X-RAY DIFFRACTIONr_bond_other_d0.0010.02868
X-RAY DIFFRACTIONr_angle_refined_deg1.491.9571327
X-RAY DIFFRACTIONr_angle_other_deg0.83232029
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4125118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.31224.34846
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00515165
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.455157
X-RAY DIFFRACTIONr_chiral_restr0.0980.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021074
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02182
X-RAY DIFFRACTIONr_nbd_refined0.2360.2153
X-RAY DIFFRACTIONr_nbd_other0.1960.2892
X-RAY DIFFRACTIONr_nbtor_refined0.1670.2439
X-RAY DIFFRACTIONr_nbtor_other0.0830.2623
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2114
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0650.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2350.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.242
X-RAY DIFFRACTIONr_mcbond_it3.4072.5771
X-RAY DIFFRACTIONr_mcbond_other1.3912.5241
X-RAY DIFFRACTIONr_mcangle_it4.0365974
X-RAY DIFFRACTIONr_scbond_it4.0482.5438
X-RAY DIFFRACTIONr_scangle_it5.695353
X-RAY DIFFRACTIONr_rigid_bond_restr2.16532222
X-RAY DIFFRACTIONr_sphericity_free10.2393193
X-RAY DIFFRACTIONr_sphericity_bonded4.04431818
LS refinement shellResolution: 1.2→1.225 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.194 92 -
Rwork0.138 1544 -
obs-1636 91.35 %
Refinement TLS params.Method: refined / Origin x: 6.6877 Å / Origin y: 15.6616 Å / Origin z: 22.1144 Å
111213212223313233
T-0.0163 Å20.0063 Å2-0.0065 Å2-0.0002 Å2-0.0035 Å2---0.0105 Å2
L0.3453 °20.0188 °2-0.0105 °2-0.6758 °2-0.2229 °2--0.4458 °2
S0.005 Å °0.0229 Å °0.0185 Å °-0.0016 Å °-0.0117 Å °0.0126 Å °-0.0175 Å °0.0054 Å °0.0067 Å °
Refinement TLS groupSelection: ALL

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