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- PDB-2bn3: Insulin before a high dose x-ray burn -

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Basic information

Entry
Database: PDB / ID: 2bn3
TitleInsulin before a high dose x-ray burn
Components(INSULIN) x 2
KeywordsRADIATION DAMAGE / SYNCHROTRON / PHASING / RIP / CARBOHYDRATE METABOLISM / GLUCOSE METABOLISM / HORMONE / INSULIN FAMILY
Function / homology
Function and homology information


estradiol secretion / positive regulation of blood circulation / negative regulation of lactation / glucose import in response to insulin stimulus / positive regulation of cell maturation / positive regulation of lactation / response to L-arginine / positive regulation of mammary gland epithelial cell proliferation / response to butyrate / negative regulation of appetite ...estradiol secretion / positive regulation of blood circulation / negative regulation of lactation / glucose import in response to insulin stimulus / positive regulation of cell maturation / positive regulation of lactation / response to L-arginine / positive regulation of mammary gland epithelial cell proliferation / response to butyrate / negative regulation of appetite / feeding behavior / response to growth hormone / response to food / positive regulation of peptide hormone secretion / positive regulation of Rho protein signal transduction / protein secretion / response to glucose / negative regulation of lipid catabolic process / positive regulation of protein secretion / insulin receptor binding / response to nutrient levels / hormone activity / positive regulation of insulin secretion / glucose metabolic process / glucose homeostasis / response to heat / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of gene expression / negative regulation of apoptotic process / 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 speciesBOS TAURUS (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.4 Å
AuthorsNanao, M.H. / Ravelli, R.B.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Improving Radiation-Damage Substructures for Rip.
Authors: Nanao, M.H. / Sheldrick, G.M. / Ravelli, R.B.
History
DepositionMar 18, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INSULIN
B: INSULIN


Theoretical massNumber of molelcules
Total (without water)5,7742
Polymers5,7742
Non-polymers00
Water1,40578
1
A: INSULIN
B: INSULIN

A: INSULIN
B: INSULIN


Theoretical massNumber of molelcules
Total (without water)11,5474
Polymers11,5474
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_565x,-y+1,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)77.900, 77.900, 77.900
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-2016-

HOH

21B-2002-

HOH

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Components

#1: Protein/peptide INSULIN


Mass: 2369.671 Da / Num. of mol.: 1 / Fragment: INSULIN A CHAIN, RESIDUES 85-105 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Organ: PANCREAS / References: UniProt: P01317
#2: Protein/peptide INSULIN


Mass: 3403.927 Da / Num. of mol.: 1 / Fragment: INSULIN B CHAIN, RESIDUES 25-54 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (domestic cattle) / Organ: PANCREAS / References: UniProt: P01317
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Compound detailsINSULIN DECREASES BLOOD GLUCOSE CONCENTRATION. IT INCREASES CELL PERMEABILITY TO MONOSACCHARIDES, ...INSULIN DECREASES BLOOD GLUCOSE CONCENTRATION. IT INCREASES CELL PERMEABILITY TO MONOSACCHARIDES, AMINO ACIDS AND FATTY ACIDS. IT ACCELERATES GLYCOLYSIS, THE PENTOSE PHOSPHATE CYCLE, AND GLYCOGEN SYNTHESIS IN LIVER
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: 3.49 Å3/Da / Density % sol: 64.51 %
Crystal growDetails: 0.4 M NAPO4/NA2HPO4 PH 10.4, 0.001 M EDTA,30%ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9392
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 18, 2004 / Details: BENT MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9392 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 24081 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.3
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.98 / % possible all: 95.9

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
SHELXEphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: OTHER / Resolution: 1.4→45 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.401 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.161 779 5 %RANDOM
Rwork0.129 ---
obs0.13 14865 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.55 Å2
Refinement stepCycle: LAST / Resolution: 1.4→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms400 0 0 78 478
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022452
X-RAY DIFFRACTIONr_bond_other_d0.0020.02386
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.963622
X-RAY DIFFRACTIONr_angle_other_deg0.9273901
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.063558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.62324.76221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5621569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg1.15151
X-RAY DIFFRACTIONr_chiral_restr0.1150.268
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02530
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0295
X-RAY DIFFRACTIONr_nbd_refined0.2810.2120
X-RAY DIFFRACTIONr_nbd_other0.2250.2428
X-RAY DIFFRACTIONr_nbtor_refined0.1950.2231
X-RAY DIFFRACTIONr_nbtor_other0.0880.2272
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2790.243
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2720.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4170.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2691.5362
X-RAY DIFFRACTIONr_mcbond_other0.8651.5119
X-RAY DIFFRACTIONr_mcangle_it2.782456
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.0213217
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.5714.5166
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.48 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.218 103 -
Rwork0.174 2150 -
obs--99.69 %

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