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- PDB-7nhu: Crystal structure of desB30 insulin produced by cell free protein... -

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Basic information

Entry
Database: PDB / ID: 7nhu
TitleCrystal structure of desB30 insulin produced by cell free protein synthesis
Components(Insulin) x 2
KeywordsHORMONE / In vitro transcription/translation / insulin / zinc-free / dimer
Function / homology
Function and homology information


negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / regulation of protein secretion / Insulin processing / positive regulation of peptide hormone secretion / positive regulation of respiratory burst ...negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / regulation of protein secretion / Insulin processing / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / negative regulation of acute inflammatory response / Regulation of gene expression in beta cells / alpha-beta T cell activation / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of protein secretion / negative regulation of gluconeogenesis / positive regulation of glycogen biosynthetic process / fatty acid homeostasis / Signal attenuation / positive regulation of insulin receptor signaling pathway / negative regulation of respiratory burst involved in inflammatory response / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of lipid catabolic process / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of protein localization to plasma membrane / nitric oxide-cGMP-mediated signaling / transport vesicle / COPI-mediated anterograde transport / positive regulation of nitric-oxide synthase activity / Insulin receptor recycling / negative regulation of reactive oxygen species biosynthetic process / positive regulation of brown fat cell differentiation / insulin-like growth factor receptor binding / NPAS4 regulates expression of target genes / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / positive regulation of cytokine production / positive regulation of glycolytic process / endosome lumen / acute-phase response / positive regulation of long-term synaptic potentiation / positive regulation of protein secretion / positive regulation of D-glucose import across plasma membrane / insulin receptor binding / positive regulation of cell differentiation / Regulation of insulin secretion / wound healing / positive regulation of neuron projection development / hormone activity / regulation of synaptic plasticity / negative regulation of protein catabolic process / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / cognition / glucose metabolic process / insulin receptor signaling pathway / cell-cell signaling / glucose homeostasis / regulation of protein localization / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / protease binding / secretory granule lumen / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / positive regulation of cell migration / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / receptor ligand activity / Amyloid fiber formation / Golgi membrane / negative regulation of gene expression / positive regulation of cell population proliferation / positive regulation of gene expression / regulation of DNA-templated transcription / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Insulin / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.4 Å
AuthorsJohansson, E.
CitationJournal: Protein Expr.Purif. / Year: 2021
Title: Cell free protein synthesis versus yeast expression - A comparison using insulin as a model protein.
Authors: Jensen, A.B. / Hubalek, F. / Stidsen, C.E. / Johansson, E. / Oberg, F.K. / Skjot, M. / Kjeldsen, T.
History
DepositionFeb 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Insulin
B: Insulin


Theoretical massNumber of molelcules
Total (without water)5,7172
Polymers5,7172
Non-polymers00
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.939, 77.939, 77.939
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Space group name HallI2b2c3
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z+1/2,x
#5: z,-x,-y+1/2
#6: -y+1/2,z,-x
#7: -z,-x+1/2,y
#8: -z+1/2,x,-y
#9: y,-z,-x+1/2
#10: x,-y,-z+1/2
#11: -x+1/2,y,-z
#12: -x,-y+1/2,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1,x+1/2
#17: z+1/2,-x+1/2,-y+1
#18: -y+1,z+1/2,-x+1/2
#19: -z+1/2,-x+1,y+1/2
#20: -z+1,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1
#22: x+1/2,-y+1/2,-z+1
#23: -x+1,y+1/2,-z+1/2
#24: -x+1/2,-y+1,z+1/2
Components on special symmetry positions
IDModelComponents
11B-115-

HOH

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Components

#1: Protein/peptide Insulin


Mass: 2383.698 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308
#2: Protein/peptide Insulin


Mass: 3332.849 Da / Num. of mol.: 1 / Mutation: des30 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 64.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium formate, 20 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.54184 Å
DetectorType: DECTRIS EIGER X 1M / Detector: PIXEL / Date: Aug 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.4→38.97 Å / Num. obs: 15199 / % possible obs: 97.1 % / Redundancy: 28.9 % / Biso Wilson estimate: 20.99 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.06932 / Rpim(I) all: 0.01238 / Rrim(I) all: 0.07046 / Net I/σ(I): 53.42
Reflection shellResolution: 1.4→1.452 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.7383 / Num. unique obs: 5656 / CC1/2: 0.657 / CC star: 0.891 / Rpim(I) all: 0.3383 / Rrim(I) all: 0.8191 / % possible all: 72.72

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6S34

6s34


Resolution: 1.4→38.97 Å / SU ML: 0.1484 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.925
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1712 1433 4.95 %
Rwork0.1587 27519 -
obs0.1593 15179 96.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.33 Å2
Refinement stepCycle: LAST / Resolution: 1.4→38.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms398 0 0 56 454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091459
X-RAY DIFFRACTIONf_angle_d1.0619630
X-RAY DIFFRACTIONf_chiral_restr0.083970
X-RAY DIFFRACTIONf_plane_restr0.006984
X-RAY DIFFRACTIONf_dihedral_angle_d6.261967
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.450.37581020.36561927X-RAY DIFFRACTION66.2
1.45-1.510.21041390.21242780X-RAY DIFFRACTION98.08
1.51-1.580.17351440.16722839X-RAY DIFFRACTION100
1.58-1.660.1961400.17632842X-RAY DIFFRACTION100
1.66-1.760.22081480.18952843X-RAY DIFFRACTION100
1.77-1.90.15441560.16622881X-RAY DIFFRACTION100
1.9-2.090.17751500.16472854X-RAY DIFFRACTION100
2.1-2.40.16461520.15462856X-RAY DIFFRACTION100
2.4-3.020.16111510.15192844X-RAY DIFFRACTION99.97
3.02-38.970.16381510.14512853X-RAY DIFFRACTION99.93
Refinement TLS params.Method: refined / Origin x: -19.4319357786 Å / Origin y: -1.43200591852 Å / Origin z: -9.23223739059 Å
111213212223313233
T0.149778361726 Å20.0070642154148 Å20.0243225879912 Å2-0.161819554015 Å20.018250149108 Å2--0.118631325339 Å2
L1.33323367245 °2-0.0401637802806 °2-0.202006844718 °2-1.2588009832 °2-0.35628750558 °2--2.75211328295 °2
S-0.00750193405913 Å °0.131344275867 Å °0.00261104851912 Å °-0.141210889564 Å °0.0468473182856 Å °0.102803721691 Å °-0.10552669277 Å °-0.165595370968 Å °-0.0433096746086 Å °
Refinement TLS groupSelection details: all

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