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- PDB-1kd7: Crystal structure of an extracellular domain fragment of human BAFF -

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Basic information

Entry
Database: PDB / ID: 1kd7
TitleCrystal structure of an extracellular domain fragment of human BAFF
ComponentsTUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B
KeywordsMEMBRANE PROTEIN / beta-sheet shandwich / TNF
Function / homology
Function and homology information


positive regulation of germinal center formation / B cell costimulation / TNFs bind their physiological receptors / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / germinal center formation / tumor necrosis factor receptor binding / B cell proliferation / B cell homeostasis / T cell proliferation / positive regulation of B cell proliferation ...positive regulation of germinal center formation / B cell costimulation / TNFs bind their physiological receptors / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / germinal center formation / tumor necrosis factor receptor binding / B cell proliferation / B cell homeostasis / T cell proliferation / positive regulation of B cell proliferation / positive regulation of T cell proliferation / tumor necrosis factor-mediated signaling pathway / T cell costimulation / B cell differentiation / cytokine activity / 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 family profile. / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor ligand superfamily member 13B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.8 Å
AuthorsKarpusas, M. / Cachero, T.G. / Qian, F. / Boriack-Sjodin, A. / Mullen, C. / Strauch, K. / Hsu, Y.-M. / Kalled, S.L.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Crystal Structure of Extracellular Human BAFF, a TNF Family Member that Stimulates B Lymphocytes
Authors: Karpusas, M. / Cachero, T.G. / Qian, F. / Boriack-Sjodin, A. / Mullen, C. / Strauch, K. / Hsu, Y.-M. / Kalled, S.L.
History
DepositionNov 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Remark 999SEQUENCE AUTHOR STATES THE SEQUENCE EQKLISEEDLNKELQGPEET IS THE N-TERMINUS (N122) CORRESPONDS TO ...SEQUENCE AUTHOR STATES THE SEQUENCE EQKLISEEDLNKELQGPEET IS THE N-TERMINUS (N122) CORRESPONDS TO RESIDUES THAT ARE NOT OBSERVED IN THE ELECTRON DENSITY. AUTHOR ALSO STATES THAT THE MYC-TAG (EQKLISEEDLNKEL) AND THE BAFF SEQUENCE FRAGMENT (QGPEET) THERE IS NO SEQUENCE MATCH FOR THE MYC-TAG BECAUSE IT IS NOT RELATED TO THE BAFF SEQUENCE, BUT IT IS A FRAGMENT OF ANOTHER PROTEIN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B
B: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B
C: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B
K: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B
L: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B
M: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B


Theoretical massNumber of molelcules
Total (without water)111,3486
Polymers111,3486
Non-polymers00
Water0
1
A: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B
B: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B
C: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B


Theoretical massNumber of molelcules
Total (without water)55,6743
Polymers55,6743
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-17 kcal/mol
Surface area17480 Å2
MethodPISA
2
K: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B
L: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B
M: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B


Theoretical massNumber of molelcules
Total (without water)55,6743
Polymers55,6743
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-17 kcal/mol
Surface area17400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.720, 121.720, 160.740
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B / BAFF / TALL-1 / TNF-and-APOL-related leukocyte expressed ligand 1


Mass: 18558.082 Da / Num. of mol.: 6 / Fragment: Extracellular domain fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Pichia pastoris (fungus) / References: UniProt: Q9Y275

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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: 3.05 Å3/Da / Density % sol: 59.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 8% PEG 4000, 0.1 M sodium acetatesolution of 8% PEG 4000, 0.1 M sodium acetate pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
19 mg/mlprotein1drop
2150 mMsodium phosphate1droppH7.
3150 mM1dropNaCl
48 %(w/v)PEG40001reservoir
50.1 Msodium acetate1reservoirpH4.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU RU20011.5418
SYNCHROTRONNSLS X4A20.9464
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV1IMAGE PLATEDec 12, 2000OSMIC BLUE OPTICS
ADSC QUANTUM 42CCDJun 4, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.94641
ReflectionResolution: 2.8→30 Å / Num. obs: 31743 / % possible obs: 95.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 14.2
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 2.9 / % possible all: 81.8
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 30 Å
Reflection shell
*PLUS
% possible obs: 81.8 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MIR / Resolution: 2.8→30 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.25 2861 RANDOM
Rwork0.217 --
all0.222 28918 -
obs0.222 28918 -
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6858 0 0 0 6858
LS refinement shellHighest resolution: 2.8 Å /
RfactorNum. reflection
Rfree0.25 2861
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 30 Å / Rfactor Rfree: 0.254 / Rfactor Rwork: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.008
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.44
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_deg26.6
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_deg0.82

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