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- PDB-1xt5: Crystal Structure of VCBP3, domain 1, from Branchiostoma floridae -

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Basic information

Entry
Database: PDB / ID: 1xt5
TitleCrystal Structure of VCBP3, domain 1, from Branchiostoma floridae
Componentsvariable region-containing chitin-binding protein 3
KeywordsIMMUNE SYSTEM / innate immunity / vcbp / primordial antigen receptor / florida lancelet / amphioxus
Function / homology
Function and homology information


endochitinase activity / chitinase / chitin catabolic process / chitin binding / extracellular region
Similarity search - Function
Chitin-binding domain type 2 / Chitin binding domain / Chitin binding Peritrophin-A domain / Chitin-binding type-2 domain profile. / Chitin binding domain superfamily / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. ...Chitin-binding domain type 2 / Chitin binding domain / Chitin binding Peritrophin-A domain / Chitin-binding type-2 domain profile. / Chitin binding domain superfamily / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBranchiostoma floridae (Florida lancelet)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.15 Å
AuthorsHernandez Prada, J.A. / Haire, R.N. / Cannon, J.P. / Allaire, M. / Jakoncic, J. / Stojanoff, V. / Litman, G.W. / Ostrov, D.A.
Citation
Journal: Nat.Immunol. / Year: 2006
Title: Ancient evolutionary origin of diversified variable regions demonstrated by crystal structures of an immune-type receptor in amphioxus.
Authors: Haire, R.N. / Allaire, M. / Jakoncic, J. / Stojanoff, V. / Cannon, J.P. / Litman, G.W. / Ostrov, D.A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystallization and preliminary X-ray analysis of VCBP3 from Branchiostoma floridae.
Authors: Hernandez Prada, J.A. / Haire, R.N. / Cannon, J.P. / Litman, G.W. / Ostrov, D.A.
History
DepositionOct 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: variable region-containing chitin-binding protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8942
Polymers14,7971
Non-polymers961
Water4,017223
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.191, 59.191, 79.263
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1143-

HOH

21A-1191-

HOH

Detailsbiological unit unknown

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Components

#1: Protein variable region-containing chitin-binding protein 3


Mass: 14797.479 Da / Num. of mol.: 1
Fragment: sequence database residues 16-150: contains immunoglobulin like region (residues 33-146)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Branchiostoma floridae (Florida lancelet)
Gene: VCBP3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8I9N0
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.708 Å3/Da / Density % sol: 54.57 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.2-1.4 M ammonium sulfate, 0.1 M NaCl, 0.1 M tris-HCl (or HEPES), 12% glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.8 / Wavelength: 0.9796, 0.97908, 0.95007
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 13, 2004
Details: Oxford Danfysik toroidal focusing mirror, Si(111) channel cut monochromator
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.81
20.97961
30.979081
40.950071
ReflectionResolution: 1.15→30 Å / Num. all: 57420 / Num. obs: 57420 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 59.3
Reflection shellResolution: 1.15→1.16 Å / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 6 / Num. unique all: 1898 / % possible all: 99.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXmodel building
SHELXL-97refinement
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.15→20 Å / Num. parameters: 11572 / Num. restraintsaints: 13947 / Isotropic thermal model: Anisotropic / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56 ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ~3%.
RfactorNum. reflection% reflectionSelection details
Rfree0.1434 5835 11.3 %RANDOM
Rwork0.1269 ---
all0.1277 51693 --
obs0.1277 51693 89.8 %-
Refine analyzeNum. disordered residues: 5 / Occupancy sum hydrogen: 904.7 / Occupancy sum non hydrogen: 1214.85
Refinement stepCycle: LAST / Resolution: 1.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1057 0 5 223 1285
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0318
X-RAY DIFFRACTIONs_zero_chiral_vol0.1
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.115
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.031
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.023
X-RAY DIFFRACTIONs_approx_iso_adps0.083
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
1.15-1.20.147X-RAY DIFFRACTION6132100
1.2-1.40.118X-RAY DIFFRACTION16692100
1.4-1.60.103X-RAY DIFFRACTION9457100
1.6-1.810.101X-RAY DIFFRACTION5898100
1.81-20.11X-RAY DIFFRACTION3449100
2-200.15X-RAY DIFFRACTION10065100

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