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- PDB-8pjc: Crystal structure of human insulin desB30 precursor with an Alani... -

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Basic information

Entry
Database: PDB / ID: 8pjc
TitleCrystal structure of human insulin desB30 precursor with an Alanine-Alanine-Lysine C-peptide in dimer (T2) conformation
ComponentsInsulin
KeywordsHORMONE / insulin / precursor / dimer
Function / homology
Function and homology information


cellular response to oxygen-containing compound / positive regulation of protein secretion / hormone activity / glucose metabolic process / glucose homeostasis / extracellular space
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: 2.14 Å
AuthorsSchluckebier, G. / Johansson, E.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Not funded Denmark
CitationJournal: Trends Biotechnol / Year: 2024
Title: Molecular engineering of insulin for recombinant expression in yeast.
Authors: Kjeldsen, T. / Andersen, A.S. / Hubalek, F. / Johansson, E. / Kreiner, F.F. / Schluckebier, G. / Kurtzhals, P.
History
DepositionJun 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model / Item: _pdbx_initial_refinement_model.entity_id_list
Revision 1.2Apr 17, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Insulin


Theoretical massNumber of molelcules
Total (without water)5,9701
Polymers5,9701
Non-polymers00
Water61334
1
A: Insulin

A: Insulin


Theoretical massNumber of molelcules
Total (without water)11,9402
Polymers11,9402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Buried area1130 Å2
ΔGint-7 kcal/mol
Surface area5860 Å2
Unit cell
Length a, b, c (Å)77.874, 77.874, 77.874
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
11A-134-

HOH

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Components

#1: Protein Insulin


Mass: 5969.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P67973
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 3.3 Å3/Da / Density % sol: 62.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: TBD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 17, 2002 / Details: mirror
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.14→99 Å / Num. obs: 4325 / % possible obs: 96.5 % / Redundancy: 2.97 % / Biso Wilson estimate: 28.02 Å2 / Rmerge(I) obs: 0.053 / Χ2: 1.45 / Net I/av σ(I): 25 / Net I/σ(I): 14.4
Reflection shellResolution: 2.14→2.22 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.256 / Num. unique obs: 1073 / Χ2: 1.49 / % possible all: 89.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-20000.93data reduction
HKL-20000.93data scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.14→18.36 Å / SU ML: 0.1421 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.1606
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.207 203 4.69 %
Rwork0.1736 4122 -
obs0.1752 4325 96.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.07 Å2
Refinement stepCycle: LAST / Resolution: 2.14→18.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms416 0 0 34 450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087425
X-RAY DIFFRACTIONf_angle_d0.7458575
X-RAY DIFFRACTIONf_chiral_restr0.051863
X-RAY DIFFRACTIONf_plane_restr0.008874
X-RAY DIFFRACTIONf_dihedral_angle_d5.867158
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.220.3154220.2213384X-RAY DIFFRACTION90.02
2.22-2.310.1938210.1752415X-RAY DIFFRACTION98.64
2.31-2.410.2568180.1831416X-RAY DIFFRACTION98.86
2.41-2.540.2106230.1891400X-RAY DIFFRACTION97.69
2.54-2.70.2052210.1604417X-RAY DIFFRACTION96.9
2.7-2.90.2056180.1731394X-RAY DIFFRACTION95.37
2.91-3.20.2506190.1573410X-RAY DIFFRACTION95.12
3.2-3.650.1783190.1697401X-RAY DIFFRACTION96.55
3.65-4.590.159200.1567439X-RAY DIFFRACTION99.14
4.6-18.360.2316220.1917446X-RAY DIFFRACTION99.15

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