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- PDB-1rj7: Crystal structure of EDA-A1 -

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Basic information

Entry
Database: PDB / ID: 1rj7
TitleCrystal structure of EDA-A1
ComponentsEctodysplasin A
KeywordsHORMONE/GROWTH FACTOR / EDA / TNF / beta-bulge / morphogen / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


trachea gland development / animal organ development / salivary gland cavitation / regulation of non-canonical NF-kappaB signal transduction / TNFs bind their physiological receptors / death receptor agonist activity / collagen trimer / tumor necrosis factor receptor binding / death receptor binding / pigmentation ...trachea gland development / animal organ development / salivary gland cavitation / regulation of non-canonical NF-kappaB signal transduction / TNFs bind their physiological receptors / death receptor agonist activity / collagen trimer / tumor necrosis factor receptor binding / death receptor binding / pigmentation / odontogenesis of dentin-containing tooth / hair follicle placode formation / canonical Wnt signaling pathway / lipid droplet / cell-matrix adhesion / cytokine activity / positive regulation of non-canonical NF-kappaB signal transduction / cytokine-mediated signaling pathway / apical part of cell / positive regulation of canonical Wnt signaling pathway / gene expression / cell differentiation / cytoskeleton / positive regulation of canonical NF-kappaB signal transduction / immune response / receptor ligand activity / signaling receptor binding / intracellular membrane-bounded organelle / positive regulation of gene expression / endoplasmic reticulum membrane / extracellular space / membrane / plasma membrane
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHymowitz, S.G. / Compaan, D.M. / Yan, M. / Ackerly, H. / Dixit, V.M. / Starovasnik, M.A. / de Vos, A.M.
CitationJournal: Structure / Year: 2003
Title: The crystal structures of EDA-A1 and EDA-A2: splice variants with distinct receptor specificity.
Authors: Hymowitz, S.G. / Compaan, D.M. / Yan, M. / Wallweber, H.J. / Dixit, V.M. / Starovasnik, M.A. / de Vos, A.M.
History
DepositionNov 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 19, 2011Group: Database references
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Aug 23, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ectodysplasin A
B: Ectodysplasin A
D: Ectodysplasin A
E: Ectodysplasin A
F: Ectodysplasin A
G: Ectodysplasin A
H: Ectodysplasin A
I: Ectodysplasin A
J: Ectodysplasin A
K: Ectodysplasin A
L: Ectodysplasin A
M: Ectodysplasin A


Theoretical massNumber of molelcules
Total (without water)214,61212
Polymers214,61212
Non-polymers00
Water6,107339
1
A: Ectodysplasin A
B: Ectodysplasin A
D: Ectodysplasin A


Theoretical massNumber of molelcules
Total (without water)53,6533
Polymers53,6533
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-24 kcal/mol
Surface area16810 Å2
MethodPISA
2
E: Ectodysplasin A
F: Ectodysplasin A
G: Ectodysplasin A


Theoretical massNumber of molelcules
Total (without water)53,6533
Polymers53,6533
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-26 kcal/mol
Surface area17400 Å2
MethodPISA
3
H: Ectodysplasin A
I: Ectodysplasin A
J: Ectodysplasin A


Theoretical massNumber of molelcules
Total (without water)53,6533
Polymers53,6533
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-22 kcal/mol
Surface area17000 Å2
MethodPISA
4
K: Ectodysplasin A
L: Ectodysplasin A
M: Ectodysplasin A


Theoretical massNumber of molelcules
Total (without water)53,6533
Polymers53,6533
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-24 kcal/mol
Surface area17010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.657, 279.687, 54.175
Angle α, β, γ (deg.)90.00, 91.36, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit is composed of 4 trimers. A trimer is the biologically relevant unit

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Components

#1: Protein
Ectodysplasin A / Ectodermal dysplasia protein / EDA protein


Mass: 17884.293 Da / Num. of mol.: 12 / Fragment: TNF domain of EDA-A1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ED1, EDA / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q92838
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 1.9 Å3/Da / Density % sol: 35 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 3350, 0.2M di-sodium hydrogen phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal grow
*PLUS
Temperature: 19 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
19.5 mg/mlprotein1drop
220 %PEG33501reservoir
30.2 Mdi-sodium hydrogen phosphate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 25, 2002
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 70270 / Num. obs: 66402 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 8.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3 / Num. unique all: 6606 / Rsym value: 0.24 / % possible all: 94.5
Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 66596 / % possible obs: 94.4 % / Num. measured all: 215586
Reflection shell
*PLUS
% possible obs: 93.1 % / Rmerge(I) obs: 0.239

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Processing

Software
NameVersionClassification
REFMAC5.1.07refinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: truncated model of Apo2L/TRAIL from 1d0g

1d0g


Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.886 / SU B: 8.162 / SU ML: 0.202 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.926 / ESU R Free: 0.307 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26029 7099 10.7 %THIN SHELLS
Rwork0.19424 ---
all0.2012 59179 --
obs0.20127 59179 94.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 6.026 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å20 Å20.1 Å2
2---0.24 Å20 Å2
3---1.18 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13548 0 0 339 13887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02213834
X-RAY DIFFRACTIONr_bond_other_d0.0020.0212449
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.93818751
X-RAY DIFFRACTIONr_angle_other_deg0.794328980
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.99851719
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.29624.253609
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.827152335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2761561
X-RAY DIFFRACTIONr_chiral_restr0.0780.22137
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215348
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022817
X-RAY DIFFRACTIONr_nbd_refined0.1970.22010
X-RAY DIFFRACTIONr_nbd_other0.2550.214127
X-RAY DIFFRACTIONr_nbtor_other0.0830.27846
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2401
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.256
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2890.2194
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.219
X-RAY DIFFRACTIONr_mcbond_it1.67258579
X-RAY DIFFRACTIONr_mcangle_it2.4613904
X-RAY DIFFRACTIONr_scbond_it2.52165255
X-RAY DIFFRACTIONr_scangle_it3.52384847
LS refinement shellResolution: 2.3→2.348 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.291 520 -
Rwork0.199 3291 -
obs--94.5 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.3322-0.32331.81942.177-0.08323.54120.06780.14360.2598-0.0609-0.1406-0.0161-0.20140.09480.07280.114-0.00930.02030.077-0.01340.114420.543513.171570.8606
24.07430.30780.23353.82710.87524.78470.1585-0.1445-0.44860.173-0.14870.26280.2546-0.3195-0.00980.1028-0.03970.00790.12610.01340.24677.9038-5.178475.8746
35.5174-1.12960.8724.5622-0.86444.91230.14440.5165-0.4524-0.2753-0.1485-0.14090.10430.32480.00410.10470.0324-0.02930.1445-0.07640.249728.9338-7.742166.8665
43.6555-0.17351.47851.8233-0.2623.13970.06210.0994-0.3167-0.1462-0.00290.07440.2836-0.0873-0.05920.1140.00590.02680.0531-0.00240.070341.014820.644652.222
53.8813-0.33640.82492.048-0.34631.4303-0.01550.26830.079-0.21020.0022-0.03380.00610.11010.01330.1127-0.00260.03420.08620.02230.016644.194540.016740.7622
63.89690.87320.91372.52980.27182.5887-0.0329-0.24520.10780.13420.00820.2632-0.0616-0.14620.02470.10990.0350.04410.04750.01120.067835.11540.433161.6959
74.25380.4096-0.91164.5235-0.22754.70790.0377-0.36620.27510.2993-0.0437-0.1718-0.18180.38290.00610.1236-0.0413-0.03070.1679-0.03850.18734.7225113.107914.3878
84.7557-0.3344-2.05272.09180.22064.4333-0.0529-0.1783-0.2547-0.1029-0.02220.09170.5380.20350.07510.21320.0241-0.01840.08590.02980.1282-2.803892.02779.9094
92.89770.4164-0.34683.3953-0.44125.37180.10020.1380.4842-0.08240.12120.4505-0.0689-0.7224-0.22140.1305-0.0048-0.03960.18060.05840.293-15.93109.92664.0483
105.6217-1.3003-1.29753.15710.33392.1657-0.00590.3027-0.0871-0.27320.04960.33710.132-0.2145-0.04370.1266-0.0311-0.03990.07710.02280.120311.741164.289416.9696
114.34750.294-1.59211.945-0.55372.96670.0485-0.19220.36970.15890.0176-0.0086-0.2628-0.0333-0.0660.12890.01160.00350.0424-0.01340.150316.971883.291228.6191
123.7683-0.7335-0.21163.1462-0.18452.1651-0.0041-0.3112-0.1380.20820.04810.14330.039-0.1328-0.0440.10260.0110.00150.10530.03550.06821.239262.603737.6252
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA247 - 39019 - 162
2X-RAY DIFFRACTION2BB247 - 39019 - 162
3X-RAY DIFFRACTION3DC247 - 39019 - 162
4X-RAY DIFFRACTION4ED242 - 39014 - 162
5X-RAY DIFFRACTION5FE247 - 39019 - 162
6X-RAY DIFFRACTION6GF247 - 39019 - 162
7X-RAY DIFFRACTION7HG247 - 38819 - 160
8X-RAY DIFFRACTION8IH247 - 38919 - 161
9X-RAY DIFFRACTION9JI248 - 39020 - 162
10X-RAY DIFFRACTION10KJ247 - 39119 - 163
11X-RAY DIFFRACTION11LK246 - 39018 - 162
12X-RAY DIFFRACTION12ML247 - 39019 - 162
Refinement
*PLUS
Lowest resolution: 20 Å / Num. reflection all: 66278 / % reflection Rfree: 10 % / Rfactor Rfree: 0.261 / Rfactor Rwork: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.28

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