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- PDB-3rto: Acoustically mounted porcine insulin microcrystals yield an X-ray... -

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Basic information

Entry
Database: PDB / ID: 3rto
TitleAcoustically mounted porcine insulin microcrystals yield an X-ray SAD structure
Components(Insulin) x 2
KeywordsHORMONE
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 / 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 / response to L-arginine / lactate biosynthetic process / positive regulation of fatty acid biosynthetic process / positive regulation of glucose metabolic process / lipoprotein biosynthetic process / COPI-mediated anterograde transport / negative regulation of glycogen catabolic process / lipid biosynthetic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / positive regulation of respiratory burst / negative regulation of acute inflammatory response / positive regulation of protein autophosphorylation / 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 / positive regulation of glycogen biosynthetic process / negative regulation of gluconeogenesis / fatty acid homeostasis / positive regulation of insulin receptor signaling pathway / 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 / acute-phase response / positive regulation of DNA replication / positive regulation of D-glucose import / positive regulation of protein secretion / insulin receptor binding / wound healing / negative regulation of protein catabolic process / hormone activity / positive regulation of protein localization to nucleus / glucose metabolic process / vasodilation / 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 / SAD / Resolution: 1.8 Å
AuthorsSoares, A.S. / Engel, M.A. / Stearns, R. / Datwani, S. / Olechno, J. / Ellson, R. / Skinner, J.M. / Allaire, M. / Orville, A.M.
CitationJournal: Biochemistry / Year: 2011
Title: Acoustically Mounted Microcrystals Yield High-Resolution X-ray Structures.
Authors: Soares, A.S. / Engel, M.A. / Stearns, R. / Datwani, S. / Olechno, J. / Ellson, R. / Skinner, J.M. / Allaire, M. / Orville, A.M.
History
DepositionMay 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 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
B: Insulin
C: Insulin
D: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7066
Polymers11,5754
Non-polymers1312
Water82946
1
A: Insulin
B: Insulin
C: Insulin
D: Insulin
hetero molecules

A: Insulin
B: Insulin
C: Insulin
D: Insulin
hetero molecules

A: Insulin
B: Insulin
C: Insulin
D: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,11818
Polymers34,72612
Non-polymers3926
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area20380 Å2
ΔGint-268 kcal/mol
Surface area12040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.700, 81.700, 33.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-31-

ZN

21D-31-

ZN

31B-32-

HOH

41B-33-

HOH

51B-34-

HOH

61D-36-

HOH

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Components

#1: Protein/peptide Insulin


Mass: 2383.698 Da / Num. of mol.: 2 / Fragment: Insulin A chain (UNP residues 88-108) / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P01315
#2: Protein/peptide Insulin


Mass: 3403.927 Da / Num. of mol.: 2 / Fragment: Insulin B chain (UNP residues 25-54) / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P01315
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 9

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Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.42 %
Crystal growMethod: small tubes / pH: 6
Details: Microcrystals are obtained by dissolving 0.025 g protein in 5 mL of crystallizing solution (200 mL 0.02 M HCl, 100 mL 0.20 M sodium citrate, 60 mL acetone, 20 mL water, 20 mL 0.12 M zinc ...Details: Microcrystals are obtained by dissolving 0.025 g protein in 5 mL of crystallizing solution (200 mL 0.02 M HCl, 100 mL 0.20 M sodium citrate, 60 mL acetone, 20 mL water, 20 mL 0.12 M zinc sulfate) at 315K. The solution is then rapidly quenched to 293K by immersing it in a cool water bath. Quenching speed determines the resulting crystal size. 20-micron crystals are obtained by quenching in a 293K water bath, 10-micron crystals by quenching in a 283K water bath, and 5-micron crystals by quenching in ice water. pH 6.0, SMALL TUBES

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
41001
1,2,3,41
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONNSLS X12B11.28
SYNCHROTRONNSLS X12C21.28
SYNCHROTRONNSLS X2531.28
SYNCHROTRONAPS 23-ID-D40.9733
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDApr 29, 2010
ADSC QUANTUM 2102CCDJul 30, 2010
ADSC QUANTUM 3153CCDFeb 27, 2010
MARMOSAIC 300 mm CCD4CCDDec 19, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
3SINGLE WAVELENGTHMx-ray1
4SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.281
20.97331
ReflectionResolution: 1.8→50 Å / Num. all: 7783 / Num. obs: 7770 / % possible obs: 99.8 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 62.2

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXSphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD
Starting model: PDB ENTRY 4INS

4ins


Resolution: 1.8→40.85 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.454 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22311 357 4.6 %RANDOM
Rwork0.18135 ---
obs0.18338 7413 99.83 %-
all-7783 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.509 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.09 Å20 Å2
2--0.18 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms806 0 2 46 854
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.022889
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.7841.9631220
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7735115
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.00324.66745
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.95415145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.064153
X-RAY DIFFRACTIONr_chiral_restr0.1340.2134
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02697
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.371.5534
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.6262864
X-RAY DIFFRACTIONr_scbond_it3.4233355
X-RAY DIFFRACTIONr_scangle_it5.7164.5348
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.435 24 -
Rwork0.314 511 -
obs--97.81 %

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