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- PDB-6or0: Crystal structure of Insulin from Non-merohedrally twinned crystals -

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Basic information

Entry
Database: PDB / ID: 6or0
TitleCrystal structure of Insulin from Non-merohedrally twinned crystals
Components
  • Insulin chain A
  • Insulin chain B
KeywordsHORMONE / Nonmerohedral twinning / twinned structure solution / twinned structure refinement
Function / homology
Function and homology information


estradiol secretion / negative regulation of lactation / positive regulation of blood circulation / 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 / negative regulation of appetite / response to butyrate ...estradiol secretion / negative regulation of lactation / positive regulation of blood circulation / 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 / negative regulation of appetite / response to butyrate / feeding behavior / response to growth hormone / response to food / positive regulation of Rho protein signal transduction / positive regulation of peptide hormone secretion / protein secretion / negative regulation of lipid catabolic process / response to glucose / response to nutrient levels / positive regulation of protein secretion / insulin receptor binding / positive regulation of insulin secretion / hormone activity / 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/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / Insulin-like superfamily
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.55 Å
AuthorsSevvana, M. / Ruf, M. / Uson, I. / Sheldrick, G.M. / Herbst-Irmer, R.
Funding support Spain, European Union, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBIO2015-64216-P Spain
European Union (EU)MDM2014-0435European Union
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Non-merohedral twinning: from minerals to proteins.
Authors: Sevvana, M. / Ruf, M. / Uson, I. / Sheldrick, G.M. / Herbst-Irmer, R.
History
DepositionApr 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)5,6722
Polymers5,6722
Non-polymers00
Water61334
1
A: Insulin chain A
B: Insulin chain B

A: Insulin chain A
B: Insulin chain B


Theoretical massNumber of molelcules
Total (without water)11,3454
Polymers11,3454
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_555-x+1/2,y,-z1
Buried area4170 Å2
ΔGint-38 kcal/mol
Surface area5530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.031, 78.031, 78.031
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-108-

HOH

21B-115-

HOH

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Components

#1: Protein/peptide Insulin chain A


Mass: 2339.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P01317
#2: Protein/peptide Insulin chain B


Mass: 3332.849 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P01317
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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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: 3.52 Å3/Da / Density % sol: 65.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10 / Details: 0.2 M Na2HPO4/Na3PO4, pH 10.0 and 0.01 M Na EDTA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER TURBO X-RAY SOURCE / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Dec 25, 2004
RadiationMonochromator: Osmic focussing mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→55.18 Å / Num. obs: 11668 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 1 % / Rsym value: 0.015 / Net I/σ(I): 62.79 / Num. measured all: 22188
Reflection shellResolution: 1.55→1.57 Å / Redundancy: 1 % / Mean I/σ(I) obs: 2.23 / Num. unique obs: 459 / Rsym value: 0.535 / % possible all: 70.8

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Processing

Software
NameClassification
SHELXrefinement
SAINTdata reduction
SADABSdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.55→55.18 Å / Cross valid method: FREE R-VALUE / σ(F): 3 / Details: NON-MEROHEDRAL TWIN REFINEMENT AGAINST HKL
RfactorNum. reflection% reflectionSelection details
Rfree0.215 588 5 %THIN SHELLS
Rwork0.166 ---
obs0.166 11080 98.4 %-
all-11080 --
Displacement parametersBiso max: 82.57 Å2 / Biso mean: 20.62 Å2 / Biso min: 10.11 Å2
Refinement stepCycle: final / Resolution: 1.55→55.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms395 0 0 34 429
Biso mean---34 -
Num. residues----50
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d1.99
X-RAY DIFFRACTIONs_similar_dist0.133
X-RAY DIFFRACTIONs_from_restr_planes0.446
X-RAY DIFFRACTIONs_zero_chiral_vol0.054
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.051
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.028
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.032
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.053
X-RAY DIFFRACTIONs_approx_iso_adps
LS refinement shellResolution: 1.55→1.61 Å /
RfactorNum. reflection
Rwork0.214 1143

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