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- PDB-5uhm: Apo-Structure of Mature Growth Differentiation Factor 11 -

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Basic information

Entry
Database: PDB / ID: 5uhm
TitleApo-Structure of Mature Growth Differentiation Factor 11
ComponentsGrowth/differentiation factor 11
KeywordsSIGNALING PROTEIN / TGFB GDF11 Apo Activin
Function / homology
Function and homology information


spinal cord anterior/posterior patterning / type B pancreatic cell maturation / negative regulation of amacrine cell differentiation / amacrine cell differentiation / camera-type eye morphogenesis / activin receptor signaling pathway / SMAD protein signal transduction / metanephros development / ureteric bud development / roof of mouth development ...spinal cord anterior/posterior patterning / type B pancreatic cell maturation / negative regulation of amacrine cell differentiation / amacrine cell differentiation / camera-type eye morphogenesis / activin receptor signaling pathway / SMAD protein signal transduction / metanephros development / ureteric bud development / roof of mouth development / mesoderm development / positive regulation of SMAD protein signal transduction / skeletal system development / cytokine activity / growth factor activity / nervous system development / cell population proliferation / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / protein-containing complex / extracellular space / nucleoplasm
Similarity search - Function
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
Growth/differentiation factor 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGoebel, E. / Thompson, T.
CitationJournal: BMC Biol. / Year: 2017
Title: Structural basis for potency differences between GDF8 and GDF11.
Authors: Walker, R.G. / Czepnik, M. / Goebel, E.J. / McCoy, J.C. / Vujic, A. / Cho, M. / Oh, J. / Aykul, S. / Walton, K.L. / Schang, G. / Bernard, D.J. / Hinck, A.P. / Harrison, C.A. / Martinez- ...Authors: Walker, R.G. / Czepnik, M. / Goebel, E.J. / McCoy, J.C. / Vujic, A. / Cho, M. / Oh, J. / Aykul, S. / Walton, K.L. / Schang, G. / Bernard, D.J. / Hinck, A.P. / Harrison, C.A. / Martinez-Hackert, E. / Wagers, A.J. / Lee, R.T. / Thompson, T.B.
History
DepositionJan 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Growth/differentiation factor 11
B: Growth/differentiation factor 11


Theoretical massNumber of molelcules
Total (without water)24,9432
Polymers24,9432
Non-polymers00
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint2 kcal/mol
Surface area10400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.160, 65.160, 101.942
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Growth/differentiation factor 11 / GDF-11 / Bone morphogenetic protein 11 / BMP-11


Mass: 12471.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GDF11, BMP11 / Production host: Escherichia coli (E. coli) / References: UniProt: O95390
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.5 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 3.75 / Details: 5mM Calcium Chloride 0.1M Sodium Acetate 33% MPD

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.10537 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 15, 2016
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.10537 Å / Relative weight: 1
ReflectionResolution: 1.9→50.97 Å / Num. obs: 20340 / % possible obs: 100 % / Redundancy: 5.8 % / Biso Wilson estimate: 35.97 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.032 / Rrim(I) all: 0.077 / Net I/σ(I): 10.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
1.9-1.945.90.7060.9630.3160.775100
9.11-50.975.20.0410.9960.0210.04799.6

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
PHASERphasing
iMOSFLM7.2.1data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E4G

5e4g


Resolution: 1.9→49.371 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.74
RfactorNum. reflection% reflection
Rfree0.2577 1007 4.99 %
Rwork0.2168 --
obs0.2186 20166 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 150.56 Å2 / Biso mean: 60.3256 Å2 / Biso min: 30.97 Å2
Refinement stepCycle: final / Resolution: 1.9→49.371 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1370 0 0 43 1413
Biso mean---57.48 -
Num. residues----174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071440
X-RAY DIFFRACTIONf_angle_d0.8531955
X-RAY DIFFRACTIONf_chiral_restr0.057195
X-RAY DIFFRACTIONf_plane_restr0.006257
X-RAY DIFFRACTIONf_dihedral_angle_d11.681888
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-2.00020.39231460.36842642278898
2.0002-2.12550.32341540.27762671282599
2.1255-2.28960.251450.23212679282499
2.2896-2.520.28851660.22442702286899
2.52-2.88460.26531430.22622728287199
2.8846-3.63420.23731200.218828132933100
3.6342-49.38750.24121330.195129243057100
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)
12.2916-1.129-0.27921.6619-0.62290.5904-0.00490.3417-0.0859-0.2844-0.0311-0.03150.3318-0.2354-0.00010.4347-0.05440.01780.3459-0.05080.3799-22.3512-10.9965-2.4206
21.6322-0.38150.69291.3428-0.6650.6511-0.00980.24170.1736-0.25710.1151-0.0369-0.4456-0.03410.00050.5291-0.0250.00320.43630.00810.4286-32.8831.877-5.3172
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 1:109)A1 - 109
2X-RAY DIFFRACTION2(chain B and resseq 1:109)B1 - 109

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