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- PDB-8pjh: Crystal structure of human insulin desB30 precursor with an Aspar... -

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Basic information

Entry
Database: PDB / ID: 8pjh
TitleCrystal structure of human insulin desB30 precursor with an Aspartate-Glycine-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 / MOLECULAR REPLACEMENT / Resolution: 1.5 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 1.3Nov 6, 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


Theoretical massNumber of molelcules
Total (without water)6,0001
Polymers6,0001
Non-polymers00
Water1,22568
1
A: Insulin

A: Insulin


Theoretical massNumber of molelcules
Total (without water)12,0002
Polymers12,0002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_455-x-1/2,y,-z1
Buried area1080 Å2
ΔGint-9 kcal/mol
Surface area6050 Å2
Unit cell
Length a, b, c (Å)78.100, 78.100, 78.100
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-124-

HOH

21A-163-

HOH

31A-165-

HOH

41A-167-

HOH

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Components

#1: Protein Insulin


Mass: 5999.851 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.: 68 / 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: 3.31 Å3/Da / Density % sol: 62.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / 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: Feb 9, 2004
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→99 Å / Num. obs: 72811 / % possible obs: 99.2 % / Redundancy: 5.7 % / Biso Wilson estimate: 23.04 Å2 / Rmerge(I) obs: 0.048 / Χ2: 1.26 / Net I/av σ(I): 15.7 / Net I/σ(I): 45.7
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.768 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1250 / Χ2: 1.09 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-20000.93data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→14.26 Å / SU ML: 0.0861 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.156
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1816 616 4.83 %
Rwork0.1719 12134 -
obs0.1723 12750 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.13 Å2
Refinement stepCycle: LAST / Resolution: 1.5→14.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms418 0 0 68 486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151451
X-RAY DIFFRACTIONf_angle_d1.1413617
X-RAY DIFFRACTIONf_chiral_restr0.066868
X-RAY DIFFRACTIONf_plane_restr0.010480
X-RAY DIFFRACTIONf_dihedral_angle_d5.512366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.650.24681740.22283005X-RAY DIFFRACTION99.94
1.65-1.890.20321490.19513007X-RAY DIFFRACTION100
1.89-2.380.17391520.17313059X-RAY DIFFRACTION100
2.38-14.260.17341410.16263063X-RAY DIFFRACTION97.3
Refinement TLS params.Method: refined / Origin x: -19.2391038276 Å / Origin y: -0.765479047723 Å / Origin z: 9.15692256171 Å
111213212223313233
T0.204635608908 Å2-0.00592210633226 Å20.0207705175243 Å2-0.211263957805 Å2-0.0265466972804 Å2--0.184814931126 Å2
L2.85109111952 °2-0.309062334226 °2-0.167844679844 °2-1.70204155419 °20.0809777096213 °2--4.79880031991 °2
S-0.0057694312883 Å °-0.168345777795 Å °0.11259966164 Å °0.198321518686 Å °0.0773147529879 Å °-0.147163236313 Å °-0.163706672535 Å °0.228432147807 Å °-0.0414272669448 Å °
Refinement TLS groupSelection details: all

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