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- PDB-2x29: Crystal structure of human4-1BB ligand ectodomain -

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Basic information

Entry
Database: PDB / ID: 2x29
TitleCrystal structure of human4-1BB ligand ectodomain
ComponentsTUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 9
KeywordsCELL ADHESION / SIGNAL-ANCHOR / CYTOKINE
Function / homology
Function and homology information


tumor necrosis factor receptor superfamily binding / positive regulation of cytotoxic T cell differentiation / TNFs bind their physiological receptors / tumor necrosis factor receptor binding / regulation of T cell proliferation / positive regulation of activated T cell proliferation / cytokine activity / cell-cell signaling / regulation of apoptotic process / immune response ...tumor necrosis factor receptor superfamily binding / positive regulation of cytotoxic T cell differentiation / TNFs bind their physiological receptors / tumor necrosis factor receptor binding / regulation of T cell proliferation / positive regulation of activated T cell proliferation / cytokine activity / cell-cell signaling / regulation of apoptotic process / immune response / signaling receptor binding / extracellular space / plasma membrane
Similarity search - Function
Tumor necrosis factor ligand superfamily member 9 / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / Tumor necrosis factor (TNF) homology domain (THD) profile. / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Jelly Rolls ...Tumor necrosis factor ligand superfamily member 9 / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / Tumor necrosis factor (TNF) homology domain (THD) 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 9
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsWon, E.Y. / Cho, H.S.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: The Structure of the Trimer of Human 4-1Bb Ligand is Unique Among Members of the Tumor Necrosis Factor Superfamily.
Authors: Won, E.Y. / Cha, K. / Byun, J.S. / Kim, D.U. / Shin, S. / Ahn, B. / Kim, Y.H. / Rice, A.J. / Walz, T. / Kwon, B.S. / Cho, H.S.
History
DepositionJan 12, 2010Deposition site: PDBE / Processing site: PDBE
SupersessionMar 23, 2010ID: 2WAK
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 9


Theoretical massNumber of molelcules
Total (without water)17,8191
Polymers17,8191
Non-polymers00
Water1,27971
1
A: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 9

A: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 9

A: TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 9


Theoretical massNumber of molelcules
Total (without water)53,4573
Polymers53,4573
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
Buried area2930 Å2
ΔGint-26.41 kcal/mol
Surface area21700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.846, 121.846, 33.575
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 9 / 4-1BB LIGAND / 4-1BBL


Mass: 17818.932 Da / Num. of mol.: 1 / Fragment: RESIDUES 80-246 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P41273
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 147 TO MET ENGINEERED RESIDUE IN CHAIN A, GLN 168 TO MET

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.03 Å3/Da / Density % sol: 69.53 % / Description: NONE
Crystal growDetails: 0.1M SODIUM CHLORIDE, 0.1M BIS-TRIS PH6.5, 1.5M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 97 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.9797
DetectorType: ADSC CCD / Detector: CCD / Date: May 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 13136 / % possible obs: 100 % / Observed criterion σ(I): 32 / Redundancy: 100 % / Rmerge(I) obs: 0.08
Reflection shellResolution: 2.3→50 Å / Redundancy: 18.7 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 32 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.3→39.88 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.911 / SU B: 4.639 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.23456 637 4.9 %RANDOM
Rwork0.21896 ---
obs0.21976 12250 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.787 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1176 0 0 71 1247
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0221200
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9051.9741629
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3175153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44222.70848
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.24415187
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.788159
X-RAY DIFFRACTIONr_chiral_restr0.1670.2188
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021901
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2721.5768
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.33421216
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.3183432
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.6524.5413
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.301→2.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 45 -
Rwork0.21 902 -
obs--99.89 %

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