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- PDB-2gyz: Crystal structure of human artemin -

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Basic information

Entry
Database: PDB / ID: 2gyz
TitleCrystal structure of human artemin
Componentsneurotrophic factor artemin isoform 3
KeywordsHORMONE/GROWTH FACTOR / neurotrophic factor / cystine-knot / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


glial cell-derived neurotrophic factor receptor binding / Peyer's patch morphogenesis / glial cell-derived neurotrophic factor receptor signaling pathway / lymphocyte migration into lymphoid organs / induction of positive chemotaxis / peripheral nervous system development / NCAM1 interactions / RET signaling / neuroblast proliferation / axon guidance ...glial cell-derived neurotrophic factor receptor binding / Peyer's patch morphogenesis / glial cell-derived neurotrophic factor receptor signaling pathway / lymphocyte migration into lymphoid organs / induction of positive chemotaxis / peripheral nervous system development / NCAM1 interactions / RET signaling / neuroblast proliferation / axon guidance / growth factor activity / receptor tyrosine kinase binding / RAF/MAP kinase cascade / signaling receptor binding / signal transduction / extracellular space / extracellular region
Similarity search - Function
Glial cell line-derived neurotrophic factor family / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsWang, X.Q. / Garcia, K.C.
CitationJournal: Structure / Year: 2006
Title: Structure of Artemin Complexed with Its Receptor GFRalpha3: Convergent Recognition of Glial Cell Line-Derived Neurotrophic Factors.
Authors: Wang, X. / Baloh, R.H. / Milbrandt, J. / Garcia, K.C.
History
DepositionMay 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: neurotrophic factor artemin isoform 3


Theoretical massNumber of molelcules
Total (without water)11,5741
Polymers11,5741
Non-polymers00
Water2,036113
1
A: neurotrophic factor artemin isoform 3

A: neurotrophic factor artemin isoform 3


Theoretical massNumber of molelcules
Total (without water)23,1492
Polymers23,1492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area3150 Å2
ΔGint-19 kcal/mol
Surface area10740 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)47.942, 47.942, 190.059
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-201-

HOH

21A-209-

HOH

31A-216-

HOH

DetailsThe biological assembly is a dimer generated from the monomer in the asymmetriun unit by the operation (X-Y, -Y, -Z) dx=0, dy=0, dz=0.

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Components

#1: Protein neurotrophic factor artemin isoform 3


Mass: 11574.299 Da / Num. of mol.: 1 / Fragment: N-terminal truncated
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5T4W7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.72 Å3/Da / Density % sol: 54.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 3 M NaNO3, 0.1 M Bis-Tris Propane (pH 7.0), VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 6, 2006
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.76→40 Å / Num. all: 15290 / Num. obs: 13668 / % possible obs: 89.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.76→1.83 Å / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCdata collection
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→40 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.824 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25462 675 5 %RANDOM
Rwork0.23949 ---
all0.243 15290 --
obs0.24027 12914 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.551 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20.38 Å20 Å2
2--0.77 Å20 Å2
3----1.15 Å2
Refinement stepCycle: LAST / Resolution: 1.76→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms735 0 0 113 848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021754
X-RAY DIFFRACTIONr_angle_refined_deg1.7821.9811022
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.769596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.46318.06531
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.59215120
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0241515
X-RAY DIFFRACTIONr_chiral_restr0.1090.2111
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02582
X-RAY DIFFRACTIONr_nbd_refined0.2730.2312
X-RAY DIFFRACTIONr_nbtor_refined0.2950.2533
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2630.273
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3240.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3150.219
X-RAY DIFFRACTIONr_mcbond_it0.971.5497
X-RAY DIFFRACTIONr_mcangle_it1.442778
X-RAY DIFFRACTIONr_scbond_it2.83282
X-RAY DIFFRACTIONr_scangle_it4.1824.5244
LS refinement shellResolution: 1.76→1.806 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 45 -
Rwork0.326 874 -
obs--95.13 %
Refinement TLS params.Method: refined / Origin x: 6.0256 Å / Origin y: 7.5997 Å / Origin z: 6.766 Å
111213212223313233
T-0.1141 Å2-0.0672 Å20.0106 Å2--0.2168 Å20.001 Å2---0.1833 Å2
L1.2513 °20.6382 °21.0352 °2-4.115 °24.7247 °2--7.5375 °2
S0.2889 Å °-0.2135 Å °0.0465 Å °0.1465 Å °-0.4629 Å °0.1459 Å °0.0161 Å °-0.3372 Å °0.174 Å °

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