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- PDB-2zp6: Crystal structure of Bovine Insulin (Hexameric form) -

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Basic information

Entry
Database: PDB / ID: 2zp6
TitleCrystal structure of Bovine Insulin (Hexameric form)
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE / Hexameric form / Carbohydrate metabolism / Cleavage on pair of basic residues / Glucose metabolism / Secreted
Function / homology
Function and homology information


estradiol secretion / positive regulation of blood circulation / negative regulation of lactation / 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 / response to butyrate / negative regulation of appetite ...estradiol secretion / positive regulation of blood circulation / negative regulation of lactation / 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 / response to butyrate / negative regulation of appetite / feeding behavior / response to growth hormone / response to food / positive regulation of peptide hormone secretion / positive regulation of Rho protein signal transduction / protein secretion / response to glucose / negative regulation of lipid catabolic process / positive regulation of protein secretion / insulin receptor binding / response to nutrient levels / 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-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily
Similarity search - Domain/homology
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsJaimohan, S.M. / Naresh, M.D. / Mandal, A.B.
Citation
Journal: To be Published
Title: Crystal structure of Bovine Insulin (Hexameric form)
Authors: Jaimohan, S.M. / Naresh, M.D. / Mandal, A.B.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: The structure of T6 bovine insulin
Authors: Smith, G.D. / Pangborn, W.A. / Blessing, R.H.
History
DepositionJun 27, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
Water63135
1
A: Insulin A chain
B: Insulin B chain
hetero molecules

A: Insulin A chain
B: Insulin B chain
hetero molecules

A: Insulin A chain
B: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4279
Polymers17,2316
Non-polymers1963
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area5590 Å2
ΔGint-94 kcal/mol
Surface area10770 Å2
MethodPISA
2
C: Insulin A chain
D: Insulin B chain
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)17,4279
Polymers17,2316
Non-polymers1963
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area5650 Å2
ΔGint-96 kcal/mol
Surface area10470 Å2
MethodPISA
3
A: Insulin A chain
B: Insulin B chain
C: Insulin A chain
D: Insulin B chain
hetero molecules

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

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)34,85418
Polymers34,46112
Non-polymers3926
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area20440 Å2
ΔGint-258 kcal/mol
Surface area12050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.465, 82.465, 33.843
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-31-

ZN

21D-31-

ZN

31D-32-

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 (domestic cattle) / Tissue: Pancreas / 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 (domestic cattle) / Tissue: Pancreas / 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


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.93 Å3/Da / Density % sol: 36.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 15% acetone, 0.6M Ammonium formate (metal basis), 0.6M sodium citrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 20, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.56→14.75 Å / Num. all: 2464 / Num. obs: 2479 / Rsym value: 0.103
Reflection shellResolution: 2.56→2.64 Å / Mean I/σ(I) obs: 4.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
AUTOMARdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A3G

2a3g


Resolution: 2.56→14.75 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.923 / SU B: 9.496 / SU ML: 0.209 / Cross valid method: THROUGHOUT / ESU R: 0.306 / ESU R Free: 0.34 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21956 283 10.3 %RANDOM
Rwork0.19788 ---
obs0.20007 2468 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.369 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.56→14.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms800 0 2 35 837
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022822
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2271.9521116
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.957598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.5124.540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.97215124
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.291152
X-RAY DIFFRACTIONr_chiral_restr0.0870.2120
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02636
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2740.2370
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2563
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.340.236
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0020.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.561.5510
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0382802
X-RAY DIFFRACTIONr_scbond_it1.1543349
X-RAY DIFFRACTIONr_scangle_it1.8174.5314
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.555→2.62 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 22 -
Rwork0.231 191 -
obs--99.53 %

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