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- PDB-2pnd: Structure or murine CRIg -

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Basic information

Entry
Database: PDB / ID: 2pnd
TitleStructure or murine CRIg
ComponentsV-set and immunoglobulin domain containing 4
KeywordsIMMUNE SYSTEM / Complement Receptor / Ig-Like domain
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsWiesmann, C.
CitationJournal: J.Exp.Med. / Year: 2007
Title: A novel inhibitor of the alternative pathway of complement reverses inflammation and bone destruction in experimental arthritis.
Authors: Katschke, K.J. / Helmy, K.Y. / Steffek, M. / Xi, H. / Yin, J. / Lee, W.P. / Gribling, P. / Barck, K.H. / Carano, R.A. / Taylor, R.E. / Rangell, L. / Diehl, L. / Hass, P.E. / Wiesmann, C. / ...Authors: Katschke, K.J. / Helmy, K.Y. / Steffek, M. / Xi, H. / Yin, J. / Lee, W.P. / Gribling, P. / Barck, K.H. / Carano, R.A. / Taylor, R.E. / Rangell, L. / Diehl, L. / Hass, P.E. / Wiesmann, C. / van Lookerenb Campagne, M.
History
DepositionApr 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)13,7621
Polymers13,7621
Non-polymers00
Water4,270237
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.334, 50.684, 62.809
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 4


Mass: 13761.718 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Vsig4, BC025105 / Production host: Escherichia coli (E. coli) / References: UniProt: Q80WA3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 1.81 Å3/Da / Density % sol: 32.1 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.5
Details: 100 mM NaCl, 25 mM TRIS, 20 % PEG 3350, 0.2 M Potassium tartrate, pH 7.5, 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: Feb 6, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 0.97→50 Å / Num. all: 60032 / Num. obs: 51825 / % possible obs: 86.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rsym value: 0.41 / Net I/σ(I): 15.7
Reflection shellResolution: 0.97→1 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.21 / % possible all: 24.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
ADSCQUANTUMdata collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ICC

2icc


Resolution: 1→39.53 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.553 / SU ML: 0.014 / Cross valid method: THROUGHOUT / ESU R: 0.023 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1416 2518 5 %RANDOM
Rwork0.12209 ---
obs0.12305 48071 92.22 %-
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: 8.979 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å20 Å2
2---0.49 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 1→39.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms968 0 0 237 1205
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021988
X-RAY DIFFRACTIONr_bond_other_d0.0020.02904
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.9431338
X-RAY DIFFRACTIONr_angle_other_deg0.83132102
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4015118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.70322.97947
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.84115181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9681510
X-RAY DIFFRACTIONr_chiral_restr0.110.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021080
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02199
X-RAY DIFFRACTIONr_nbd_refined0.2090.2145
X-RAY DIFFRACTIONr_nbd_other0.2040.2901
X-RAY DIFFRACTIONr_nbtor_refined0.1690.2439
X-RAY DIFFRACTIONr_nbtor_other0.0840.2647
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2160
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2640.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2750.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.266
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4362.5786
X-RAY DIFFRACTIONr_mcbond_other1.3372.5244
X-RAY DIFFRACTIONr_mcangle_it3.8235968
X-RAY DIFFRACTIONr_scbond_it3.6272.5455
X-RAY DIFFRACTIONr_scangle_it5.0065370
X-RAY DIFFRACTIONr_rigid_bond_restr2.05132306
X-RAY DIFFRACTIONr_sphericity_free9.513237
X-RAY DIFFRACTIONr_sphericity_bonded3.67631872
LS refinement shellResolution: 1→1.021 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.274 80 -
Rwork0.218 1380 -
obs--45.1 %
Refinement TLS params.Method: refined / Origin x: 9.0292 Å / Origin y: 28.7997 Å / Origin z: 9.376 Å
111213212223313233
T-0.0148 Å2-0.0016 Å2-0.0029 Å2--0.0059 Å20.0009 Å2---0.012 Å2
L0.32 °20.0187 °20.0986 °2-0.675 °2-0.0593 °2--0.2671 °2
S0.0251 Å °-0.0197 Å °-0.0072 Å °-0.0044 Å °-0.0188 Å °0.0339 Å °0.0151 Å °0.0066 Å °-0.0063 Å °

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