- PDB-5hly: Structure of Pro-Activin A Precursor at 2.3 A Resolution -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 5hly
Title
Structure of Pro-Activin A Precursor at 2.3 A Resolution
Components
Inhibin beta A chain
Keywords
SIGNALING PROTEIN / Growth factor / Precursor / Signalling
Function / homology
Function and homology information
activin A complex / inhibin A complex / cardiac fibroblast cell development / negative regulation of B cell differentiation / regulation of follicle-stimulating hormone secretion / positive regulation of ovulation / GABAergic neuron differentiation / Antagonism of Activin by Follistatin / negative regulation of follicle-stimulating hormone secretion / progesterone secretion ...activin A complex / inhibin A complex / cardiac fibroblast cell development / negative regulation of B cell differentiation / regulation of follicle-stimulating hormone secretion / positive regulation of ovulation / GABAergic neuron differentiation / Antagonism of Activin by Follistatin / negative regulation of follicle-stimulating hormone secretion / progesterone secretion / type II activin receptor binding / striatal medium spiny neuron differentiation / Glycoprotein hormones / negative regulation of macrophage differentiation / cellular response to oxygen-glucose deprivation / positive regulation of follicle-stimulating hormone secretion / hemoglobin biosynthetic process / cellular response to follicle-stimulating hormone stimulus / cellular response to cholesterol / eyelid development in camera-type eye / Signaling by BMP / activin receptor signaling pathway / negative regulation of phosphorylation / SMAD protein signal transduction / Signaling by Activin / mesodermal cell differentiation / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / cellular response to angiotensin / odontogenesis / hair follicle development / positive regulation of transcription by RNA polymerase III / negative regulation of G1/S transition of mitotic cell cycle / response to aldosterone / roof of mouth development / endodermal cell differentiation / peptide hormone binding / positive regulation of SMAD protein signal transduction / negative regulation of type II interferon production / positive regulation of collagen biosynthetic process / hematopoietic progenitor cell differentiation / extrinsic apoptotic signaling pathway / ovarian follicle development / positive regulation of protein metabolic process / erythrocyte differentiation / positive regulation of erythrocyte differentiation / cytokine activity / growth factor activity / hormone activity / negative regulation of cell growth / defense response / cytokine-mediated signaling pathway / autophagy / male gonad development / cell-cell signaling / cellular response to hypoxia / nervous system development / transcription by RNA polymerase II / positive regulation of ERK1 and ERK2 cascade / cell differentiation / cell surface receptor signaling pathway / positive regulation of protein phosphorylation / negative regulation of cell population proliferation / regulation of transcription by RNA polymerase II / positive regulation of gene expression / positive regulation of DNA-templated transcription / protein-containing complex binding / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / identical protein binding Similarity search - Function
Inhibin, beta A subunit / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Cystine-knot cytokine Similarity search - Domain/homology
Resolution: 2.3→2.38 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.687 / Mean I/σ(I) obs: 2.4 / % possible all: 37.1
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Processing
Software
Name
Version
Classification
PHENIX
(1.10pre_2084: ???)
refinement
XDS
datareduction
Aimless
datascaling
PHASER
phasing
Coot
modelbuilding
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: experimental phases from separate dataset Resolution: 2.302→74.15 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 2.05 / Phase error: 22.9 / Details: anomalous Se signal used in refinement
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2524
977
5.17 %
Random selection
Rwork
0.2025
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-
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obs
0.2049
11167
79.06 %
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Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parameters
Biso mean: 44.07 Å2
Refinement step
Cycle: LAST / Resolution: 2.302→74.15 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2372
0
1
25
2398
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.003
2424
X-RAY DIFFRACTION
f_angle_d
0.724
3262
X-RAY DIFFRACTION
f_dihedral_angle_d
18.534
1515
X-RAY DIFFRACTION
f_chiral_restr
0.032
362
X-RAY DIFFRACTION
f_plane_restr
0.003
419
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.3022-2.4236
0.2752
79
0.2526
1206
X-RAY DIFFRACTION
38
2.4236-2.5755
0.4056
94
0.2522
1616
X-RAY DIFFRACTION
50
2.5755-2.7743
0.2854
133
0.2464
2195
X-RAY DIFFRACTION
69
2.7743-3.0535
0.2442
186
0.2169
3146
X-RAY DIFFRACTION
98
3.0535-3.4954
0.2405
173
0.2059
3248
X-RAY DIFFRACTION
100
3.4954-4.4037
0.2408
154
0.1781
3252
X-RAY DIFFRACTION
100
4.4037-74.192
0.243
158
0.1982
3260
X-RAY DIFFRACTION
100
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