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- PDB-4m4m: The structure of Ni T6 bovine insulin -

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Basic information

Entry
Database: PDB / ID: 4m4m
TitleThe structure of Ni T6 bovine insulin
Components(Insulin) x 2
KeywordsHORMONE / Nickel 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
NICKEL (II) ION / Insulin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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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)11,6056
Polymers11,4874
Non-polymers1172
Water1,44180
1
A: Insulin
B: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8023
Polymers5,7442
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-15 kcal/mol
Surface area3680 Å2
MethodPISA
2
C: Insulin
D: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8023
Polymers5,7442
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-15 kcal/mol
Surface area3550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.850, 80.850, 33.360
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-

NI

21D-101-

NI

31D-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-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 1.83 Å3/Da / Density % sol: 32.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.05M sodium citrate, 15%(v/v) acetone, 15mM nickel(II)acetate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 15, 2011
RadiationMonochromator: Bent Si (111) crystal, horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.5→16.783 Å / Num. all: 13016 / Num. obs: 12710 / % possible obs: 97.6 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -3
Reflection shellResolution: 1.5→1.54 Å / % possible all: 79.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
PHENIX(phenix.refine: 2010_07_29_2140)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→16.78 Å / SU ML: 0.4 / σ(F): 1.99 / Phase error: 35.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2243 636 5 %Random
Rwork0.1819 ---
obs0.1842 12710 97.69 %-
all-13016 --
Solvent computationShrinkage radii: 0.29 Å / VDW probe radii: 0.5 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.238 Å2 / ksol: 0.51 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.3806 Å2-0 Å2-0 Å2
2--1.3806 Å2-0 Å2
3----2.7611 Å2
Refinement stepCycle: LAST / Resolution: 1.5→16.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms800 0 2 80 882
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016852
X-RAY DIFFRACTIONf_angle_d1.4841152
X-RAY DIFFRACTIONf_dihedral_angle_d17.327302
X-RAY DIFFRACTIONf_chiral_restr0.085127
X-RAY DIFFRACTIONf_plane_restr0.007151
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.61570.50921210.50822291X-RAY DIFFRACTION93
1.6157-1.77820.32571290.25572465X-RAY DIFFRACTION100
1.7782-2.03510.22971290.17452440X-RAY DIFFRACTION100
2.0351-2.56260.20851300.13952482X-RAY DIFFRACTION99
2.5626-16.78410.17271270.14212396X-RAY DIFFRACTION97
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)
13.94170.4155-0.95841.81562.33233.57480.1511-0.38420.1914-0.34840.13530.1146-1.08760.1054-0.21430.3617-0.02280.03490.1769-0.01670.1415-8.640411.39324.3499
22.4432-0.6885-0.65192.87440.05830.3664-0.00460.28340.00570.2179-0.0113-0.1199-0.0846-0.0209-0.01430.13230.050.05520.1476-0.00180.2204-16.057712.053815.5567
30.67810.17970.41020.17540.00280.3721-0.00720.1094-0.1081-0.01770.06660.00960.1122-0.0208-0.00010.09230.00810.01940.13470.00480.1441-6.72876.925412.3003
40.4177-0.1975-0.20830.110.22381.48790.0712-0.0654-0.01610.07270.05890.143-0.3668-0.0754-0.11590.18550.00920.03540.10780.02220.1556-4.345816.94610.8966
54.05061.7159-0.55521.7712-1.88173.1243-0.52550.38380.4381-0.16690.26060.0596-0.10960.08560.20820.2488-0.0752-0.00150.26220.08770.25752.220414.3687-1.9531
60.39820.5510.76431.87170.36022.82430.0480.0970.0358-0.24770.25460.07430.03050.3064-0.20010.2055-0.0416-0.00520.1851-0.03230.15578.269818.07696.7894
71.38480.85210.91360.60210.41550.87740.0781-0.1128-0.167-0.0166-0.0352-0.14230.0529-0.1226-0.02020.0875-0.00240.02940.10120.01180.13472.43439.377510.2766
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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