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- PDB-4lsd: Myokine structure -

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Basic information

Entry
Database: PDB / ID: 4lsd
TitleMyokine structure
ComponentsFibronectin type III domain-containing protein 5
KeywordsHORMONE / myokine / metabolism
Function / homology
Function and homology information


response to muscle activity / peroxisomal membrane / positive regulation of brown fat cell differentiation / hormone activity / membrane => GO:0016020 / endoplasmic reticulum / extracellular region / plasma membrane
Similarity search - Function
Fibronectin type III domain-containing protein 5, C-terminal domain / Domain of unknown function (DUF4808) / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like ...Fibronectin type III domain-containing protein 5, C-terminal domain / Domain of unknown function (DUF4808) / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fibronectin type III domain-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.28 Å
AuthorsSchumacher, M.A. / Ohashi, T. / Shah, R.S. / Chinnam, N. / Erickson, H.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: The structure of irisin reveals a novel intersubunit beta-sheet fibronectin type III (FNIII) dimer: implications for receptor activation.
Authors: Schumacher, M.A. / Chinnam, N. / Ohashi, T. / Shah, R.S. / Erickson, H.P.
History
DepositionJul 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Apr 3, 2024Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fibronectin type III domain-containing protein 5
B: Fibronectin type III domain-containing protein 5
C: Fibronectin type III domain-containing protein 5
D: Fibronectin type III domain-containing protein 5
E: Fibronectin type III domain-containing protein 5
F: Fibronectin type III domain-containing protein 5
G: Fibronectin type III domain-containing protein 5
H: Fibronectin type III domain-containing protein 5


Theoretical massNumber of molelcules
Total (without water)89,7318
Polymers89,7318
Non-polymers00
Water4,288238
1
A: Fibronectin type III domain-containing protein 5
B: Fibronectin type III domain-containing protein 5


Theoretical massNumber of molelcules
Total (without water)22,4332
Polymers22,4332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-4 kcal/mol
Surface area10450 Å2
MethodPISA
2
C: Fibronectin type III domain-containing protein 5
D: Fibronectin type III domain-containing protein 5


Theoretical massNumber of molelcules
Total (without water)22,4332
Polymers22,4332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-6 kcal/mol
Surface area10090 Å2
MethodPISA
3
G: Fibronectin type III domain-containing protein 5
H: Fibronectin type III domain-containing protein 5


Theoretical massNumber of molelcules
Total (without water)22,4332
Polymers22,4332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-3 kcal/mol
Surface area10120 Å2
MethodPISA
4
E: Fibronectin type III domain-containing protein 5
F: Fibronectin type III domain-containing protein 5


Theoretical massNumber of molelcules
Total (without water)22,4332
Polymers22,4332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.200, 93.200, 284.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Fibronectin type III domain-containing protein 5 / Fibronectin type III repeat-containing protein 2 / Irisin


Mass: 11216.376 Da / Num. of mol.: 8 / Fragment: UNP residues 33-130
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FNDC5, FRCP2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NAU1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 3.45 Å3/Da / Density % sol: 64.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: citrate, cacodylate buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 13, 2013
RadiationMonochromator: si (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.28→66.52 Å / Num. all: 58408 / Num. obs: 53502 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 47.3 Å2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: SIRAS
Starting model: thimerosal derivative

Resolution: 2.28→66.52 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2853600.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.236 6312 11.8 %RANDOM
Rwork0.224 ---
obs0.224 53502 91.6 %-
all-58408 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.8233 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 51.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.89 Å20 Å20 Å2
2--2.89 Å20 Å2
3----5.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.28→66.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5987 0 0 238 6225
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d26.5
X-RAY DIFFRACTIONc_improper_angle_d1.25
LS refinement shellResolution: 2.28→2.42 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.378 567 8.9 %
Rwork0.36 5826 -
obs--67.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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