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- PDB-6q8q: Bovine Insulin under 2 kbar of argon -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6q8q
TitleBovine Insulin under 2 kbar of argon
Components(Insulin) x 2
KeywordsHORMONE / insulin / argon / high pressure
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 / response to glucose / negative regulation of lipid catabolic process / response to nutrient levels / positive regulation of protein secretion / insulin receptor binding / 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/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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsPrange, T. / Carpentier, P.
Citation
Journal: To be published
Title: Argon-labelling protein crystals by high pressure cooling at 2 kbar
Authors: Prange, T. / Carpentier, P.
#1: Journal: Journal of Applied Crystallography / Year: 2016
Title: Gas-sensitive biological crystals processed in pressurized oxygen and krypton atmospheres: deciphering gas channels in proteins using a novel soak-and-freeze methodology
Authors: Lafumat, B. / Mueller-Dieckmann, C. / Leonard, G. / Colloc'h, N. / Prange, T. / Giraud, T. / Dobias, F. / Royant, A. / van der Linden, P. / Carpentier, P.
History
DepositionDec 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Insulin
B: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8143
Polymers5,7742
Non-polymers401
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-15 kcal/mol
Surface area3370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.559, 77.559, 77.559
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein/peptide Insulin /


Mass: 2369.671 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Insulin chain A / Source: (natural) Bos taurus (cattle) / References: UniProt: P01317
#2: Protein/peptide Insulin /


Mass: 3403.927 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P01317
#3: Chemical ChemComp-AR / ARGON / Argon


Mass: 39.948 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ar
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 3.55 Å3/Da / Density % sol: 65.5 % / Description: COLORLESS PRISMATIC
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PROTEIN DROP: 10 MG/ML. RESERVOIR: 1.2 M TMAO + 0.1 M SODIUM MALATE, PH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.9997 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 27, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.9997 Å / Relative weight: 1
ReflectionResolution: 2→39 Å / Num. obs: 5259 / % possible obs: 97.8 % / Redundancy: 30.4 % / Biso Wilson estimate: 22.3 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.016 / Rrim(I) all: 0.081 / Net I/σ(I): 31.3
Reflection shellResolution: 2→2.11 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 7.8 / Num. unique obs: 673 / Rpim(I) all: 0.087 / Rrim(I) all: 0.218 / % possible all: 85.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XSCALEdata scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3BN3

3bn3


Resolution: 2→38.81 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.947 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.123
RfactorNum. reflection% reflectionSelection details
Rfree0.199 265 5.1 %RANDOM
Rwork0.18164 ---
obs0.18262 4969 97.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.976 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→38.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms402 0 1 37 440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.012417
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7741.637566
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.974549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.52224.09122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.5491565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.254151
X-RAY DIFFRACTIONr_chiral_restr0.1380.250
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02331
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_it3.2412.626202
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.673.849249
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.3533.15214
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined9.88135.581632
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: 2.004→2.056 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 17 -
Rwork0.304 291 -
obs--76.62 %

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