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- PDB-5e4g: Crystal structure of human growth differentiation factor 11 (GDF-11) -

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Basic information

Entry
Database: PDB / ID: 5e4g
TitleCrystal structure of human growth differentiation factor 11 (GDF-11)
ComponentsGrowth/differentiation factor 11
KeywordsHORMONE / Bone morphogenetic protein 11 / BMP-11 / GDF 11 / growth factor
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 / SMAD protein signal transduction / metanephros development / ureteric bud development / roof of mouth development / mesoderm development ...spinal cord anterior/posterior patterning / type B pancreatic cell maturation / negative regulation of amacrine cell differentiation / amacrine cell differentiation / camera-type eye morphogenesis / SMAD protein signal transduction / metanephros development / ureteric bud development / roof of mouth development / mesoderm development / 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 Cytokines, subunit B ...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 Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
Growth/differentiation factor 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsPadyana, A.K. / Vaidialingam, B. / Hayes, D.B. / Gupta, P. / Franti, M. / Farrow, N.A.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Crystal structure of human GDF11.
Authors: Padyana, A.K. / Vaidialingam, B. / Hayes, D.B. / Gupta, P. / Franti, M. / Farrow, N.A.
History
DepositionOct 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Growth/differentiation factor 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8603
Polymers12,4711
Non-polymers3882
Water2,558142
1
A: Growth/differentiation factor 11
hetero molecules

A: Growth/differentiation factor 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7206
Polymers24,9432
Non-polymers7774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)32.270, 32.270, 210.602
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-309-

HOH

21A-389-

HOH

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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.: 1 / Fragment: UNP residues 299-407
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: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.22 Å3/Da / Density % sol: 44.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.18 M magnesium acetate, 0.1 M HEPES, pH 7.5, 22.5% PEG3350, 0.01 M strontium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→22.82 Å / Num. obs: 17599 / % possible obs: 92.3 % / Redundancy: 3.11 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.056 / Χ2: 1.14 / Net I/σ(I): 9.4 / Num. measured all: 56267 / Scaling rejects: 1548
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
1.5-1.553.010.561.9527517011.3915791.8
1.55-1.623.240.4862.4575517221.417492.1
1.62-1.693.190.3812.9571817351.2819293.7
1.69-1.783.090.3173.5545017221.3212693.3
1.78-1.893.030.2155.1540717201.2519691.2
1.89-2.043.160.156.9580417781.118295.2
2.04-2.243.090.1069.5568218010.9912595.5
2.24-2.563.080.08211.6572118180.9211593.9
2.56-3.233.10.05617.3577918390.858793.4
3.23-22.823.110.03431.7567617630.919483.4

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: homology model

Resolution: 1.5→22.818 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2071 880 5.01 %RANDOM
Rwork0.188 16683 --
obs0.189 17563 92.05 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.26 Å2 / Biso mean: 28.5419 Å2 / Biso min: 14.57 Å2
Refinement stepCycle: final / Resolution: 1.5→22.818 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms859 0 26 142 1027
Biso mean--46.73 38.56 -
Num. residues----108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006961
X-RAY DIFFRACTIONf_angle_d1.0581293
X-RAY DIFFRACTIONf_chiral_restr0.074126
X-RAY DIFFRACTIONf_plane_restr0.006171
X-RAY DIFFRACTIONf_dihedral_angle_d13.487367
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4998-1.59370.29681410.27792678281991
1.5937-1.71670.26781440.24652738288293
1.7167-1.88940.241440.2422725286992
1.8894-2.16270.24141500.20142845299595
2.1627-2.7240.22671510.19592864301594
2.724-22.82080.1671500.15542833298387
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)
18.66830.3998-1.16514.09242.49774.3231-0.0871-0.07220.28180.09640.02570.1562-0.0531-0.15710.0740.1597-0.0088-0.00880.2267-0.00830.201-12.546210.31260.1914
20.97980.10821.19470.80580.05462.3442-0.0653-0.083-0.04320.08510.02680.0342-0.0754-0.24830.05660.17210.0090.00880.1846-0.00860.1711-2.821610.304117.2877
34.2064-2.2203-2.11941.8083-0.76257.07630.14960.51720.2497-0.1666-0.09550.21210.3081-0.6204-0.02110.194-0.01660.00190.2418-0.02450.2041-2.57475.417-8.9335
41.7741-1.0187-1.05990.89821.72475.1103-0.04130.1065-0.26180.1514-0.05250.21770.4909-0.26910.06090.1995-0.02470.00110.19260.00170.21861.6731-0.0841-8.5855
51.31220.7452.52740.89531.75256.3240.0150.0981-0.03260.10680.0863-0.1006-0.0240.2953-0.08820.1861-0.0093-0.00410.1783-0.01540.19198.395112.974617.0806
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 15 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 44 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 45 through 55 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 56 through 78 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 79 through 109 )A0

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