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- PDB-2g4m: Insulin collected at 2.0 A wavelength -

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Basic information

Entry
Database: PDB / ID: 2g4m
TitleInsulin collected at 2.0 A wavelength
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE/GROWTH FACTOR / insulin at 2.0 A wavelength / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


positive regulation of lipoprotein lipase activity / 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 ...positive regulation of lipoprotein lipase activity / 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 / lactate biosynthetic process / positive regulation of glucose metabolic process / positive regulation of fatty acid biosynthetic process / lipoprotein biosynthetic process / COPI-mediated anterograde transport / 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 / lipid biosynthetic process / positive regulation of respiratory burst / negative regulation of acute inflammatory response / alpha-beta T cell activation / positive regulation of dendritic spine maintenance / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / negative regulation of gluconeogenesis / positive regulation of insulin receptor signaling pathway / positive regulation of glycogen biosynthetic process / fatty acid homeostasis / negative regulation of lipid catabolic process / regulation of protein localization to plasma membrane / nitric oxide-cGMP-mediated signaling / negative regulation of reactive oxygen species biosynthetic process / insulin-like growth factor receptor binding / neuron projection maintenance / positive regulation of mitotic nuclear division / positive regulation of glycolytic process / positive regulation of cytokine production / positive regulation of DNA replication / acute-phase response / positive regulation of protein secretion / positive regulation of D-glucose import / insulin receptor binding / wound healing / hormone activity / negative regulation of protein catabolic process / positive regulation of protein localization to nucleus / vasodilation / glucose metabolic process / insulin receptor signaling pathway / glucose homeostasis / protease binding / positive regulation of canonical NF-kappaB signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / positive regulation of cell migration / G protein-coupled receptor signaling pathway / negative regulation of gene expression / positive regulation of cell population proliferation / 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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsMueller-Dieckmann, C. / Weiss, M.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: On the routine use of soft X-rays in macromolecular crystallography. Part IV. Efficient determination of anomalous substructures in biomacromolecules using longer X-ray wavelengths.
Authors: Mueller-Dieckmann, C. / Panjikar, S. / Schmidt, A. / Mueller, S. / Kuper, J. / Geerlof, A. / Wilmanns, M. / Singh, R.K. / Tucker, P.A. / Weiss, M.S.
History
DepositionFeb 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Insulin A chain
B: Insulin B chain


Theoretical massNumber of molelcules
Total (without water)5,7882
Polymers5,7882
Non-polymers00
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-14 kcal/mol
Surface area3430 Å2
MethodPISA
2
A: Insulin A chain
B: Insulin B chain

A: Insulin A chain
B: Insulin B chain


Theoretical massNumber of molelcules
Total (without water)11,5754
Polymers11,5754
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_565x,-y+1,-z+1/21
Buried area4300 Å2
ΔGint-36 kcal/mol
Surface area5620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.270, 78.270, 78.270
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
11A-42-

HOH

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Components

#1: Protein/peptide Insulin A chain


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


Mass: 3403.927 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P01315
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 2 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 7537 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
CCP4(SCALA)data scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.756 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22295 173 2.3 %RANDOM
Rwork0.16651 ---
obs0.1677 7364 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.011 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms403 0 0 61 464
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.022423
X-RAY DIFFRACTIONr_bond_other_d0.0030.02359
X-RAY DIFFRACTIONr_angle_refined_deg1.7771.952575
X-RAY DIFFRACTIONr_angle_other_deg0.9053836
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.061549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.35724.28621
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1531565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.127151
X-RAY DIFFRACTIONr_chiral_restr0.1190.262
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02470
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0291
X-RAY DIFFRACTIONr_nbd_refined0.20.289
X-RAY DIFFRACTIONr_nbd_other0.1810.2340
X-RAY DIFFRACTIONr_nbtor_refined0.1950.2199
X-RAY DIFFRACTIONr_nbtor_other0.0920.2246
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2310.233
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2370.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3980.215
X-RAY DIFFRACTIONr_mcbond_it2.0061.5326
X-RAY DIFFRACTIONr_mcbond_other0.3031.5109
X-RAY DIFFRACTIONr_mcangle_it2.562.5406
X-RAY DIFFRACTIONr_scbond_it4.8665219
X-RAY DIFFRACTIONr_scangle_it5.64510169
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.509 10 -
Rwork0.45 535 -
obs--99.27 %
Refinement TLS params.Method: refined / Origin x: 20.4067 Å / Origin y: 38.7807 Å / Origin z: 28.4551 Å
111213212223313233
T-0.0988 Å20.0013 Å20.0254 Å2--0.0845 Å20.0283 Å2---0.1235 Å2
L2.6472 °21.3211 °2-1.3599 °2-4.9821 °20.8709 °2--7.4904 °2
S0.1211 Å °0.0039 Å °0.1894 Å °0.1686 Å °-0.0026 Å °0.2397 Å °-0.1548 Å °-0.3079 Å °-0.1185 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 211 - 21
2X-RAY DIFFRACTION1BB1 - 301 - 30

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