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- PDB-5mr9: Ligand-receptor complex. -

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Basic information

Entry
Database: PDB / ID: 5mr9
TitleLigand-receptor complex.
ComponentsNeurturin
KeywordsSIGNALING PROTEIN / Complex / Signalling / Receptor
Function / homology
Function and homology information


glial cell-derived neurotrophic factor receptor binding / nerve development / NCAM1 interactions / neural crest cell migration / RET signaling / growth factor activity / receptor tyrosine kinase binding / cell surface receptor protein tyrosine kinase signaling pathway / neuron projection development / MAPK cascade ...glial cell-derived neurotrophic factor receptor binding / nerve development / NCAM1 interactions / neural crest cell migration / RET signaling / growth factor activity / receptor tyrosine kinase binding / cell surface receptor protein tyrosine kinase signaling pathway / neuron projection development / MAPK cascade / nervous system development / RAF/MAP kinase cascade / axon / signaling receptor binding / extracellular region
Similarity search - Function
Glial cell line-derived neurotrophic factor 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: 2.4 Å
AuthorsSandmark, J. / Oster, L. / Aagaard, A. / Roth, R.G. / Dahl, G.
CitationJournal: To Be Published
Title: Structure and biophysical characterisation of the human complex - a role for heparan sulfate
Authors: Sandmark, J. / Dahl, G. / Oster, L. / Xu, B. / Johansson, P. / Akerud, T. / Aagaard, A. / Davidsson, P. / Sorhede-Winzell, M. / Rainey, G.J. / Roth, R.G.
History
DepositionDec 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neurturin
B: Neurturin


Theoretical massNumber of molelcules
Total (without water)23,4132
Polymers23,4132
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-8 kcal/mol
Surface area11660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.080, 32.750, 61.910
Angle α, β, γ (deg.)90.00, 107.06, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein Neurturin /


Mass: 11706.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NRTN / Production host: Escherichia coli (E. coli) / References: UniProt: Q99748
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.45 Å3/Da / Density % sol: 49.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 10.5 / Details: 40% MPD and 100 mM CAPS pH 10.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.992 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.992 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 8997 / % possible obs: 99.9 % / Redundancy: 4.6 % / Biso Wilson estimate: 55.4 Å2 / Net I/σ(I): 6.7

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Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→48.15 Å / Cor.coef. Fo:Fc: 0.9074 / Cor.coef. Fo:Fc free: 0.8848 / SU R Cruickshank DPI: 0.498 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.507 / SU Rfree Blow DPI: 0.294 / SU Rfree Cruickshank DPI: 0.296
RfactorNum. reflection% reflectionSelection details
Rfree0.2885 427 4.75 %RANDOM
Rwork0.248 ---
obs0.25 8996 99.81 %-
Displacement parametersBiso mean: 50.97 Å2
Baniso -1Baniso -2Baniso -3
1-8.3341 Å20 Å2-3.3731 Å2
2---3.1199 Å20 Å2
3----5.2142 Å2
Refinement stepCycle: 1 / Resolution: 2.4→48.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1627 0 0 34 1661
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081661HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.062242HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d618SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes34HARMONIC2
X-RAY DIFFRACTIONt_gen_planes264HARMONIC5
X-RAY DIFFRACTIONt_it1661HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.44
X-RAY DIFFRACTIONt_other_torsion23.33
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion197SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1710SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.68 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3728 130 5.12 %
Rwork0.3686 2408 -
all0.3688 2538 -
obs--99.81 %

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