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- PDB-4m4h: Radiation damage study of Cu T6-insulin - 0.06 MGy -

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Basic information

Entry
Database: PDB / ID: 4m4h
TitleRadiation damage study of Cu T6-insulin - 0.06 MGy
Components(Insulin) x 2
KeywordsHORMONE / Copper binding
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
COPPER (II) ION / Insulin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFrankaer, C.G. / Harris, P. / Stahl, K.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Towards accurate structural characterization of metal centres in protein crystals: the structures of Ni and Cu T6 bovine insulin derivatives.
Authors: Frankaer, C.G. / Mossin, S. / Stahl, K. / Harris, P.
History
DepositionAug 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source

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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)11,6146
Polymers11,4874
Non-polymers1272
Water93752
1
A: Insulin
B: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8073
Polymers5,7442
Non-polymers641
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-16 kcal/mol
Surface area3580 Å2
MethodPISA
2
C: Insulin
D: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8073
Polymers5,7442
Non-polymers641
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-15 kcal/mol
Surface area3570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.658, 80.658, 33.333
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-101-

CU

21D-101-

CU

31B-220-

HOH

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Components

#1: Protein/peptide Insulin /


Mass: 2339.645 Da / Num. of mol.: 2 / Fragment: INSULIN A CHAIN (UNP RESIDUES 85-105) / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P01317
#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) Bos taurus (cattle) / References: UniProt: P01317
#3: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 1.82 Å3/Da / Density % sol: 32.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 0.05M sodium citrate, 15%(v/v) acetone, 7.5mM copper(II)acetate, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Jun 14, 2013
RadiationMonochromator: Multilayered mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→16.75 Å / Num. all: 6370 / Num. obs: 6342 / % possible obs: 99.6 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -3
Reflection shellResolution: 1.9→1.97 Å / % possible all: 99.1

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Processing

Software
NameVersionClassification
CrysalisProdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
CrysalisProdata reduction
CrysalisProdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→16.75 Å / SU ML: 0.22 / σ(F): 2.01 / Phase error: 26.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2195 293 4.62 %Random
Rwork0.1655 ---
obs0.1682 6340 99.65 %-
all-6370 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→16.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms794 0 2 52 848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007838
X-RAY DIFFRACTIONf_angle_d1.0081131
X-RAY DIFFRACTIONf_dihedral_angle_d15.171293
X-RAY DIFFRACTIONf_chiral_restr0.074125
X-RAY DIFFRACTIONf_plane_restr0.004147
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.39320.27541480.19983025X-RAY DIFFRACTION100
2.3932-16.75040.19781450.15113022X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.323-2.6856-1.23887.75750.82745.95210.18640.3721-0.84530.2579-0.2305-0.22151.3503-0.2628-0.03720.44290.015-0.0310.2017-0.05520.2429-8.734-11.5821-13.2919
27.2720.62562.82028.9895-8.14179.47590.0895-0.2991-0.2098-0.3393-0.18420.00330.7494-0.44750.09910.1441-0.0848-0.04680.1911-0.00320.2768-16.0471-12.0653-4.3848
35.42240.3776-5.82633.3897-2.87058.12440.022-0.54530.1533-0.0548-0.1406-0.0038-0.07170.39170.09540.0727-0.0052-0.02490.12050.02180.0972-6.414-6.8873-1.3567
45.265-2.0103-2.40552.8887-1.31995.68960.0030.2667-0.1427-0.26440.17490.28620.7306-0.4991-0.18250.2005-0.0466-0.03850.09630.02930.1008-4.2711-16.97640.2332
58.30325.20493.11768.28564.56742.8786-0.1648-1.1002-0.47261.1041-0.193-0.34740.5187-0.10850.39430.34640.05940.0070.3620.07360.15572.4724-14.346613.0976
67.22642.92352.46935.83452.05113.50960.12170.1493-0.37610.23960.3829-0.28590.23110.9122-0.42750.39510.09910.0630.2803-0.00280.18248.4481-18.18784.2937
74.9789-2.6839-3.3537.01445.67234.9070.2166-0.03710.0947-0.0734-0.0528-0.1035-0.02580.0547-0.12350.13830.0182-0.01960.07540.01460.1072.284-9.42550.7816
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1:8 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 13:19 )
3X-RAY DIFFRACTION3CHAIN B AND (RESID 9:18 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 23:27 ) OR CHAIN D AND (RESID 23:27 )
5X-RAY DIFFRACTION5CHAIN C AND (RESID 1:8 )
6X-RAY DIFFRACTION6CHAIN C AND (RESID 13:19 )
7X-RAY DIFFRACTION7CHAIN D AND (RESID 9:18)

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