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- PDB-1b18: PH AFFECTS GLU B13 SWITCHING AND SULFATE BINDING IN CUBIC INSULIN... -

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Basic information

Entry
Database: PDB / ID: 1b18
TitlePH AFFECTS GLU B13 SWITCHING AND SULFATE BINDING IN CUBIC INSULIN CRYSTALS (PH 5.53 COORDINATES)
Components
  • PROTEIN (INSULIN a chain)
  • PROTEIN (INSULIN b chain)
KeywordsHORMONE/GROWTH FACTOR / HORMONE / GLUCOSE CONCENTRATION DECREASE / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


Insulin processing / IRS activation / Signal attenuation / Insulin receptor signalling cascade / Signaling by Insulin receptor / Synthesis, secretion, and deacylation of Ghrelin / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Insulin receptor recycling / glycoprotein biosynthetic process / response to L-arginine ...Insulin processing / IRS activation / Signal attenuation / Insulin receptor signalling cascade / Signaling by Insulin receptor / Synthesis, secretion, and deacylation of Ghrelin / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Insulin receptor recycling / glycoprotein biosynthetic process / response to L-arginine / positive regulation of lipoprotein lipase activity / lactate biosynthetic process / positive regulation of fatty acid biosynthetic process / positive regulation of glucose metabolic process / lipoprotein biosynthetic process / COPI-mediated anterograde transport / lipid biosynthetic process / negative regulation of gluconeogenesis / positive regulation of insulin receptor signaling pathway / positive regulation of protein autophosphorylation / insulin-like growth factor receptor binding / positive regulation of DNA replication / positive regulation of protein secretion / hormone activity / glucose metabolic process / insulin receptor signaling pathway / glucose homeostasis / positive regulation of cell migration / extracellular space / 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 speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.8 Å
AuthorsDiao, J.S. / Caspar, D.L.D.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Crystallographic titration of cubic insulin crystals: pH affects GluB13 switching and sulfate binding.
Authors: Diao, J.
#1: Journal: Biophys.J. / Year: 1992
Title: Conformational Changes in Cubic Insulin Crystals in the Ph Range 7-11
Authors: Gursky, O. / Badger, J. / Li, Y. / Caspar, D.L.
#2: Journal: Biophys.J. / Year: 1992
Title: Monovalent Cation Binding in Cubic Insulin Crystals
Authors: Gursky, O. / Li, Y. / Badger, J. / Caspar, D.L.
#3: Journal: Biophys.J. / Year: 1992
Title: Flexibility in Crystalline Insulins
Authors: Badger, J.
#4: Journal: Acta Crystallogr.,Sect.B / Year: 1991
Title: Structure of the Pig Insulin Dimer in the Cubic Crystal
Authors: Badger, J. / Harris, M.R. / Reynolds, C.D. / Evans, A.C. / Dodson, E.J. / Dodson, G.G. / North, A.C.T.
#5: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991
Title: Water Structure in Cubic Insulin Crystals
Authors: Badger, J. / Caspar, D.L.
#6: Journal: J.Mol.Biol. / Year: 1978
Title: Zinc-Free Cubic Pig Insulin: Crystallization and Structure Determination
Authors: Dodson, E.J. / Dodson, G.G. / Lewitova, A. / Sabesan, M.
History
DepositionNov 26, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 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: PROTEIN (INSULIN a chain)
B: PROTEIN (INSULIN b chain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8843
Polymers5,7882
Non-polymers961
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-26 kcal/mol
Surface area3470 Å2
MethodPISA
2
A: PROTEIN (INSULIN a chain)
B: PROTEIN (INSULIN b chain)
hetero molecules

A: PROTEIN (INSULIN a chain)
B: PROTEIN (INSULIN b chain)
hetero molecules

A: PROTEIN (INSULIN a chain)
B: PROTEIN (INSULIN b chain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6519
Polymers17,3636
Non-polymers2883
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area6750 Å2
ΔGint-116 kcal/mol
Surface area8660 Å2
MethodPISA
3
A: PROTEIN (INSULIN a chain)
B: PROTEIN (INSULIN b chain)
hetero molecules

A: PROTEIN (INSULIN a chain)
B: PROTEIN (INSULIN b chain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7676
Polymers11,5754
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_565x,-y+1,-z+1/21
Buried area4670 Å2
ΔGint-58 kcal/mol
Surface area5610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.717, 78.717, 78.717
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11B-133-

HOH

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Components

#1: Protein/peptide PROTEIN (INSULIN a chain)


Mass: 2383.698 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P01315
#2: Protein/peptide PROTEIN (INSULIN b chain)


Mass: 3403.927 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P01315
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 3.51 Å3/Da / Density % sol: 65 % / Description: RAXIS-II
Crystal growpH: 5.53 / Details: pH 5.53
Components of the solutionsConc.: 2 / Name: 1M SODIUM SULFATE SOLUTION AT PH 5.53 / Details: 3 / Volume: 1 Å3
Crystal grow
*PLUS
pH: 9.2 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.05 Msodium phosphate11
20.001 Msodium EDTA11pH11
318 mg/mlprotein11
40.15 Msodium phosphate12
50.001 Msodium EDTA12pH9.2

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceWavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→55 Å / Num. obs: 9061 / % possible obs: 99.6 % / Redundancy: 3.79 % / Biso Wilson estimate: 20.05 Å2 / Rsym value: 0.094
Reflection
*PLUS
Highest resolution: 1.8 Å / % possible obs: 99.7 % / Rmerge(I) obs: 0.094

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.843refinement
X-PLORphasing
RefinementMethod to determine structure: OTHER / Resolution: 1.8→10 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.216 771 10.1 %RANDOM
Rwork0.1835 ---
obs-7510 98.35 %-
Displacement parametersBiso mean: 21.7 Å2
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms403 0 5 64 472
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.14
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.89
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.13
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.8→1.84 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.3359 46 9.16 %
Rwork0.2867 451 -
obs--99 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3SO4.PARSO4.TOP
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 10 Å / Rfactor Rfree: 0.2173 / Rfactor Rwork: 0.1839
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.89
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.13

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