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- PDB-1kxg: The 2.0 Ang Resolution Structure of BLyS, B Lymphocyte Stimulator. -

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Basic information

Entry
Database: PDB / ID: 1kxg
TitleThe 2.0 Ang Resolution Structure of BLyS, B Lymphocyte Stimulator.
ComponentsB lymphocyte stimulator
KeywordsCYTOKINE / BAFF / TALL-1 / THANK / zTNF4 / TNF superfamily / jellyroll / beta-sandwich
Function / homology
Function and homology information


B cell costimulation / positive regulation of germinal center formation / TNFs bind their physiological receptors / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / transitional one stage B cell differentiation / tumor necrosis factor receptor binding / germinal center formation / skin development / B cell homeostasis / B cell proliferation ...B cell costimulation / positive regulation of germinal center formation / TNFs bind their physiological receptors / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / transitional one stage B cell differentiation / tumor necrosis factor receptor binding / germinal center formation / skin development / B cell homeostasis / B cell proliferation / T cell proliferation / T cell costimulation / positive regulation of B cell proliferation / positive regulation of T cell proliferation / cytokine activity / tumor necrosis factor-mediated signaling pathway / TNFR2 non-canonical NF-kB pathway / receptor ligand activity / signaling receptor binding / focal adhesion / intracellular membrane-bounded organelle / perinuclear region of cytoplasm / signal transduction / extracellular space / extracellular region / membrane / plasma membrane / cytoplasm
Similarity search - Function
: / TNF(Tumour Necrosis Factor) family / Jelly Rolls - #40 / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Tumour necrosis factor-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / 1,4-DIETHYLENE DIOXIDE / Tumor necrosis factor ligand superfamily member 13B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsOren, D.A. / Li, Y. / Volovik, Y. / Morris, T.S. / Dharia, C. / Das, K. / Galperina, O. / Gentz, R. / Arnold, E.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Structural basis of BLyS receptor recognition.
Authors: Oren, D.A. / Li, Y. / Volovik, Y. / Morris, T.S. / Dharia, C. / Das, K. / Galperina, O. / Gentz, R. / Arnold, E.
History
DepositionJan 31, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: B lymphocyte stimulator
B: B lymphocyte stimulator
C: B lymphocyte stimulator
D: B lymphocyte stimulator
E: B lymphocyte stimulator
F: B lymphocyte stimulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,65535
Polymers102,3396
Non-polymers2,31629
Water8,323462
1
A: B lymphocyte stimulator
B: B lymphocyte stimulator
C: B lymphocyte stimulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,60421
Polymers51,1693
Non-polymers1,43518
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8200 Å2
ΔGint27 kcal/mol
Surface area17490 Å2
MethodPISA
2
D: B lymphocyte stimulator
E: B lymphocyte stimulator
F: B lymphocyte stimulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,05114
Polymers51,1693
Non-polymers88211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7340 Å2
ΔGint7 kcal/mol
Surface area17900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.580, 123.580, 161.230
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
DetailsThe biologically active form is a trimer and two complete trimers are found in the asymmetric unit.

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Components

#1: Protein
B lymphocyte stimulator / BLyS / Tumor necrosis factor ligand superfamily member 13B


Mass: 17056.443 Da / Num. of mol.: 6 / Fragment: soluble portion (residues 134-285)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9Y275
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C4H8O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / 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: 3.6 Å3/Da / Density % sol: 66 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 25% dioxane, 25 mM MgCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 279.0K
Crystal grow
*PLUS
pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
225 mMsodium citrate1drop
3125 mM1droppH6.NaCl
425 %(v/v)dioxane1drop
525 mM1dropMgCl2
625 %dioxane1reservoir
725 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.942 / Wavelength: 0.942 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 13, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.942 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 93234 / % possible obs: 99.3 % / Observed criterion σ(I): -1 / Redundancy: 20.8 % / Rsym value: 0.083 / Net I/σ(I): 23.4
Reflection shellResolution: 2→2.08 Å / Mean I/σ(I) obs: 3.8 / Rsym value: 0.384 / % possible all: 93.8
Reflection
*PLUS
Highest resolution: 2 Å / Num. measured all: 1940104 / Rmerge(I) obs: 0.083
Reflection shell
*PLUS
Highest resolution: 2 Å / % possible obs: 93.8 % / Num. unique obs: 9746 / Rmerge(I) obs: 0.384

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1D0G

1d0g


Resolution: 2→24.64 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3298001.29 / Data cutoff high rms absF: 3298001.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: Residues 204-206 in all six chains have very poor electron density.
RfactorNum. reflection% reflectionSelection details
Rfree0.209 1849 2 %RANDOM
Rwork0.189 ---
obs-93180 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.31 Å2 / ksol: 0.352931 e/Å3
Displacement parametersBaniso 13: 0 Å2 / Baniso 23: 0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2→24.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6858 0 153 462 7473
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.571.5
X-RAY DIFFRACTIONc_mcangle_it2.522
X-RAY DIFFRACTIONc_scbond_it2.272
X-RAY DIFFRACTIONc_scangle_it3.522.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.243 282 1.9 %
Rwork0.223 14664 -
obs--95.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CIT+DIO.PARAMCIT+DIO.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 25 Å / Rfactor obs: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.72
X-RAY DIFFRACTIONc_mcbond_it1.571.5
X-RAY DIFFRACTIONc_scbond_it2.272
X-RAY DIFFRACTIONc_mcangle_it2.522
X-RAY DIFFRACTIONc_scangle_it3.522.5
LS refinement shell
*PLUS
Rfactor obs: 0.223

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