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- PDB-5xpv: Structure of the V domain of amphioxus IgVJ-C2 -

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Basic information

Entry
Database: PDB / ID: 5xpv
TitleStructure of the V domain of amphioxus IgVJ-C2
Componentsamphioxus IgVJ-C2
KeywordsIMMUNE SYSTEM / Immunoglobulin superfamily / dimmer
Function / homology
Function and homology information


dendrite self-avoidance / cell-cell adhesion mediator activity / homophilic cell adhesion via plasma membrane adhesion molecules / axon guidance / axon / plasma membrane
Similarity search - Function
Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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
Similarity search - Domain/homology
Ig-like domain-containing protein
Similarity search - Component
Biological speciesBranchiostoma floridae (Florida lancelet)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsChen, R. / Qi, J. / Zhang, N. / Zhang, L. / Yao, S. / Wu, Y. / Jiang, B. / Wang, Z. / Yuan, H. / Zhang, Q. / Xia, C.
Funding support China, 2items
OrganizationGrant numberCountry
the China Ministry of Science and Technology2013CB835302 China
the State Key Program of the National Natural Science Foundation of China31230074 China
CitationJournal: J. Immunol. / Year: 2018
Title: Discovery and Analysis of Invertebrate IgVJ-C2 Structure from Amphioxus Provides Insight into the Evolution of the Ig Superfamily.
Authors: Chen, R. / Zhang, L. / Qi, J. / Zhang, N. / Zhang, L. / Yao, S. / Wu, Y. / Jiang, B. / Wang, Z. / Yuan, H. / Zhang, Q. / Xia, C.
History
DepositionJun 5, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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

Downloads & links

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Assembly

Deposited unit
A: amphioxus IgVJ-C2
B: amphioxus IgVJ-C2


Theoretical massNumber of molelcules
Total (without water)22,4342
Polymers22,4342
Non-polymers00
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-8 kcal/mol
Surface area9730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.412, 67.785, 74.625
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11B-299-

HOH

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Components

#1: Protein amphioxus IgVJ-C2 / amphioxus IgVJ-C2


Mass: 11217.116 Da / Num. of mol.: 2 / Fragment: V domain, UNP RESIDUES 20-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Branchiostoma floridae (Florida lancelet)
Gene: BRAFLDRAFT_122935 / Production host: Escherichia coli 042 (bacteria) / Strain (production host): 042 / References: UniProt: C3ZN36
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.56 Å3/Da / Density % sol: 51.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.5M ammonium sulfate, 0.1M sodium citrate tribasic dehydrate, 1.0M lithium sulfate monohydrate (pH 5.6)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jan 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 18794 / % possible obs: 99.9 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 35.7
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.186 / Num. measured obs: 18784

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XPW

5xpw


Resolution: 1.9→23.352 Å / SU ML: 0.16 / Cross valid method: NONE / σ(F): 1.37 / Phase error: 21.04
RfactorNum. reflection% reflection
Rfree0.2067 966 5.16 %
Rwork0.1796 --
obs0.181 18730 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→23.352 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1580 0 0 202 1782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051614
X-RAY DIFFRACTIONf_angle_d0.8192192
X-RAY DIFFRACTIONf_dihedral_angle_d14.798570
X-RAY DIFFRACTIONf_chiral_restr0.036234
X-RAY DIFFRACTIONf_plane_restr0.004296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.899-1.99910.24221570.19532425X-RAY DIFFRACTION99
1.9991-2.12420.18871320.17592510X-RAY DIFFRACTION100
2.1242-2.28810.20851360.17382498X-RAY DIFFRACTION100
2.2881-2.51810.19581240.18472551X-RAY DIFFRACTION100
2.5181-2.88190.2381460.18852524X-RAY DIFFRACTION100
2.8819-3.62870.19511410.18112551X-RAY DIFFRACTION100
3.6287-23.3540.19911300.17282705X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -11.3577 Å / Origin y: 14.3008 Å / Origin z: -22.9049 Å
111213212223313233
T0.1734 Å2-0.0141 Å2-0.0058 Å2-0.1645 Å2-0.0024 Å2--0.1778 Å2
L0.3642 °2-0.0984 °2-0.3794 °2-0.2117 °2-0.0989 °2--0.8937 °2
S0.0179 Å °0.02 Å °-0.0146 Å °0.0045 Å °0.0024 Å °-0.0106 Å °-0.0427 Å °-0.0168 Å °-0.0001 Å °
Refinement TLS groupSelection details: all

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