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- PDB-3bj9: Crystal structure of the Surrogate Light Chain Variable Domain VpreBJ -

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Basic information

Entry
Database: PDB / ID: 3bj9
TitleCrystal structure of the Surrogate Light Chain Variable Domain VpreBJ
ComponentsImmunoglobulin iota chain, Immunoglobulin lambda-like polypeptide 1
KeywordsIMMUNE SYSTEM / immunoglobulin domain / beta sheet / Polymorphism
Function / homology
Function and homology information


Cell surface interactions at the vascular wall / immune response / endoplasmic reticulum / extracellular space / extracellular region
Similarity search - Function
: / 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 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
Immunoglobulin iota chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsMorstadt, L.M. / Bohm, A.A. / Stollar, B.D. / Baleja, J.D.
CitationJournal: Protein Sci. / Year: 2008
Title: Engineering and characterization of a single chain surrogate light chain variable domain.
Authors: Morstadt, L. / Bohm, A. / Yuksel, D. / Kumar, K. / Stollar, B.D. / Baleja, J.D.
History
DepositionDec 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 4, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.type
Revision 1.3Sep 4, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_special_symmetry / reflns / reflns_shell
Item: _reflns.pdbx_Rsym_value / _reflns_shell.pdbx_Rsym_value
Revision 1.4Nov 13, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ref_seq_dif.details / _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
1: Immunoglobulin iota chain, Immunoglobulin lambda-like polypeptide 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1244
Polymers12,9381
Non-polymers1863
Water2,000111
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.811, 67.176, 99.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
111-101-

ARG

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Components

#1: Antibody Immunoglobulin iota chain, Immunoglobulin lambda-like polypeptide 1 / Vpre / B protein / VpreB protein / CD179a antigen / Immunoglobulin-related protein 14.1 / ...Vpre / B protein / VpreB protein / CD179a antigen / Immunoglobulin-related protein 14.1 / Immunoglobulin omega polypeptide / Ig lambda-5 / CD179b antigen


Mass: 12937.543 Da / Num. of mol.: 1
Fragment: Fusion protein consists of Ig domain of VPREB protein and J-fragment of Ig lambda-5
Mutation: Ig domain of VpreB fused to J-segment of 14.1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VPREB1, VPREB / Plasmid: pIg203 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE)pLysE / References: UniProt: P12018
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE 14 RESIDUES: THVFGSGTQLTVLS BELONG TO THE "J-SEGMENT, FUSED TO THE IG DOMAIN OF VPREB"

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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: 2.84 Å3/Da / Density % sol: 56.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Imidazole, 1M Sodium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418
DetectorType: OXFORD / Detector: CCD / Date: Nov 30, 2006 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→55.73 Å / Num. all: 9774 / Num. obs: 9712 / % possible obs: 99.36 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 7.3 / % possible all: 92.38

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
MOLREPphasing
REFMAC5.2.0003refinement
PDB_EXTRACT3.004data extraction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→15.97 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.895 / SU B: 3.25 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23015 519 5.1 %RANDOM
Rwork0.18096 ---
obs0.18338 9712 99.36 %-
all-9774 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.819 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2→15.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms960 0 12 111 1083
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211000
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6221.9411361
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg15.5675129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.45322.548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.72415158
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7621511
X-RAY DIFFRACTIONr_chiral_restr0.1340.2141
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02792
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2210.2438
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.2655
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2110
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2810.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8311.5632
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3442989
X-RAY DIFFRACTIONr_scbond_it1.7543425
X-RAY DIFFRACTIONr_scangle_it2.5444.5368
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 44 -
Rwork0.183 635 -
obs--92.38 %

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