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- PDB-4e7t: The structure of T6 bovine insulin -

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Basic information

Entry
Database: PDB / ID: 4e7t
TitleThe structure of T6 bovine insulin
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE / Zinc 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
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsHarris, P. / Frankaer, C.G. / Knudsen, M.V.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: The structures of T(6), T(3)R(3) and R(6) bovine insulin: combining X-ray diffraction and absorption spectroscopy.
Authors: Frankar, C.G. / Knudsen, M.V. / Noren, K. / Nazarenko, E. / Stahl, K. / Harris, P.
History
DepositionMar 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Insulin A chain
B: Insulin B chain
C: Insulin A chain
D: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6186
Polymers11,4874
Non-polymers1312
Water1,51384
1
A: Insulin A chain
B: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8093
Polymers5,7442
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-16 kcal/mol
Surface area3670 Å2
MethodPISA
2
C: Insulin A chain
D: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8093
Polymers5,7442
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-15 kcal/mol
Surface area3590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.980, 80.980, 33.490
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-

ZN

21D-101-

ZN

31B-216-

HOH

41B-217-

HOH

51D-228-

HOH

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Components

#1: Protein/peptide Insulin A chain


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


Mass: 3403.927 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P01317
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 1.84 Å3/Da / Density % sol: 33.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.05M sodium citrate, 0.5mM zinc acetate, 15% acetone, pH 7.2, 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: May 17, 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: 1.4→20.78 Å / Num. all: 15790 / Num. obs: 15790 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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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
Starting model: PDB ENTRY 1MSO

1mso


Resolution: 1.4→20.78 Å / SU ML: 0.2 / σ(F): 1.99 / Phase error: 24.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2285 790 5 %RANDOM
Rwork0.1938 ---
obs0.1956 15790 98.15 %-
all-15790 --
Solvent computationShrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.952 Å2 / ksol: 0.533 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.35 Å20 Å2-0 Å2
2--2.35 Å2-0 Å2
3----4.7001 Å2
Refinement stepCycle: LAST / Resolution: 1.4→20.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms800 0 2 84 886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013844
X-RAY DIFFRACTIONf_angle_d1.4491140
X-RAY DIFFRACTIONf_dihedral_angle_d14.996296
X-RAY DIFFRACTIONf_chiral_restr0.093127
X-RAY DIFFRACTIONf_plane_restr0.008148
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4002-1.4880.3191320.29472511X-RAY DIFFRACTION100
1.488-1.60280.32431340.25182547X-RAY DIFFRACTION100
1.6028-1.7640.26641340.23312543X-RAY DIFFRACTION100
1.764-2.01910.251320.21112506X-RAY DIFFRACTION98
2.0191-2.54310.21641340.17542537X-RAY DIFFRACTION99
2.5431-20.78670.20521240.17672356X-RAY DIFFRACTION92
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)
10.45130.7141-0.9412.5402-1.05372.0981-0.04780.1568-0.02830.42420.28690.23440.2715-0.5759-0.20870.2993-0.0699-0.01280.34220.03080.1791-5.6424-13.16162.4143
20.58440.0751-0.00320.0489-0.12370.5671-0.1505-0.14050.18890.01050.03130.08340.22890.05970.07420.2697-0.0254-0.0210.11930.05150.2467-2.398-19.9496-6.406
31.3849-1.2539-0.70751.63781.85653.29030.1371-0.03190.1592-0.0696-0.1262-0.318-0.3128-0.11390.00160.1342-0.0008-0.02320.09680.0140.1412-2.6733-9.3043-9.6614
42.49121.29881.41091.95151.31921.06730.1604-0.3297-0.09750.3619-0.0983-0.19250.5197-0.1732-0.10230.2017-0.0529-0.03740.1790.00910.1692-12.6171-12.1795-11.0497
54.7918-3.1562-1.4962.4426-0.23084.71250.23941.176-0.59320.0702-0.37430.3187-0.2137-0.29080.08840.20450.0241-0.09830.404-0.05970.2712-13.64-5.1364-24.0086
63.1533-2.21581.05873.13410.39981.18480.24880.0693-0.2112-0.15840.21590.1713-0.1683-0.2255-0.33820.12910.01580.03430.255-0.00840.1912-19.8835-1.8239-15.2708
70.3618-0.4915-0.20520.75820.12790.357-0.0676-0.00370.09060.01690.0827-0.09960.0252-0.007-0.02410.14460.0047-0.0120.15630.02410.1812-9.5061-2.3383-11.5104
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
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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