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- PDB-1wav: CRYSTAL STRUCTURE OF FORM B MONOCLINIC CRYSTAL OF INSULIN -

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Basic information

Entry
Database: PDB / ID: 1wav
TitleCRYSTAL STRUCTURE OF FORM B MONOCLINIC CRYSTAL OF INSULIN
Components(INSULIN) x 2
KeywordsHORMONE / INSULIN / PHENOL
Function / homology
Function and homology information


Insulin processing / IRS activation / Signal attenuation / Insulin receptor signalling cascade / Signaling by Insulin receptor / Synthesis, secretion, and deacylation of Ghrelin / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Insulin receptor recycling / glycoprotein biosynthetic process / response to L-arginine ...Insulin processing / IRS activation / Signal attenuation / Insulin receptor signalling cascade / Signaling by Insulin receptor / Synthesis, secretion, and deacylation of Ghrelin / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Insulin receptor recycling / glycoprotein biosynthetic process / response to L-arginine / positive regulation of lipoprotein lipase activity / lactate biosynthetic process / lipoprotein biosynthetic process / positive regulation of fatty acid biosynthetic process / positive regulation of glucose metabolic process / COPI-mediated anterograde transport / lipid biosynthetic process / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / positive regulation of respiratory burst / positive regulation of dendritic spine maintenance / alpha-beta T cell activation / negative regulation of acute inflammatory response / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / fatty acid homeostasis / positive regulation of glycogen biosynthetic process / positive regulation of DNA replication / negative regulation of gluconeogenesis / positive regulation of nitric oxide mediated signal transduction / regulation of protein localization to plasma membrane / negative regulation of lipid catabolic process / positive regulation of insulin receptor signaling pathway / negative regulation of reactive oxygen species biosynthetic process / positive regulation of protein autophosphorylation / insulin-like growth factor receptor binding / neuron projection maintenance / positive regulation of glycolytic process / positive regulation of mitotic nuclear division / positive regulation of cytokine production / acute-phase response / positive regulation of protein secretion / positive regulation of glucose import / negative regulation of proteolysis / wound healing / insulin receptor binding / negative regulation of protein catabolic process / hormone activity / vasodilation / positive regulation of protein localization to nucleus / glucose metabolic process / glucose homeostasis / insulin receptor signaling pathway / protease binding / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell migration / G protein-coupled receptor signaling pathway / negative regulation of gene expression / positive regulation of cell population proliferation / 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 speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsLiang, D.-C. / Ding, J.-H. / Chang, W.-R. / Wan, Z.-L.
Citation
Journal: Sci.China, Ser.C: Life Sci. / Year: 1996
Title: Molecular replacement study on form-B monoclinic crystal of insulin.
Authors: Ding, J. / Wan, Z. / Chang, W. / Liang, D.
#1: Journal: Sci.China,Ser.B / Year: 1994
Title: Phase Relationship in Phenol-Insulin Crystal Growth System
Authors: Liang, D.-C. / Song, L.-Z. / Wan, Z.-L. / Chang, W.-R.
#2: Journal: Chin.Sci.Bull. / Year: 1993
Title: Preliminary Crystallographic Studies on a New Monoclinic Crystal Form of Phenol-Insulin
Authors: Song, L.-Z. / Wan, Z.-L. / Chang, W.-R. / Liang, D.-C.
#3: Journal: Sci.China,Ser.B / Year: 1989
Title: Crystal Structure Determination of 4-Zinc Bovine Insulin at 1.9 A Resolution
Authors: Li, M. / Wang, D.C. / Liang, D.C.
History
DepositionFeb 28, 1996-
Revision 1.0Feb 28, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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
E: INSULIN
F: INSULIN
G: INSULIN
H: INSULIN
I: INSULIN
J: INSULIN
K: INSULIN
L: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,42120
Polymers34,72612
Non-polymers6958
Water2,018112
1
A: INSULIN
B: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,9474
Polymers5,7882
Non-polymers1602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-14 kcal/mol
Surface area4200 Å2
MethodPISA
2
C: INSULIN
D: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,9474
Polymers5,7882
Non-polymers1602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-15 kcal/mol
Surface area4140 Å2
MethodPISA
3
E: INSULIN
F: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8823
Polymers5,7882
Non-polymers941
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-13 kcal/mol
Surface area4120 Å2
MethodPISA
4
G: INSULIN
H: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,9764
Polymers5,7882
Non-polymers1882
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-10 kcal/mol
Surface area4250 Å2
MethodPISA
5
I: INSULIN
J: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8823
Polymers5,7882
Non-polymers941
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-11 kcal/mol
Surface area4170 Å2
MethodPISA
6
K: INSULIN
L: INSULIN


Theoretical massNumber of molelcules
Total (without water)5,7882
Polymers5,7882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-12 kcal/mol
Surface area4410 Å2
MethodPISA
7


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19320 Å2
ΔGint-206 kcal/mol
Surface area13510 Å2
MethodPISA
8
A: INSULIN
B: INSULIN
E: INSULIN
F: INSULIN
I: INSULIN
J: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,71110
Polymers17,3636
Non-polymers3484
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-93 kcal/mol
Surface area10580 Å2
MethodPISA
9
C: INSULIN
D: INSULIN
G: INSULIN
H: INSULIN
K: INSULIN
L: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,71110
Polymers17,3636
Non-polymers3484
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint-91 kcal/mol
Surface area11000 Å2
MethodPISA
10
A: INSULIN
B: INSULIN
C: INSULIN
D: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8948
Polymers11,5754
Non-polymers3194
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-36 kcal/mol
Surface area6950 Å2
MethodPISA
11
E: INSULIN
F: INSULIN
G: INSULIN
H: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8587
Polymers11,5754
Non-polymers2823
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-31 kcal/mol
Surface area6650 Å2
MethodPISA
12
I: INSULIN
J: INSULIN
K: INSULIN
L: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6695
Polymers11,5754
Non-polymers941
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-30 kcal/mol
Surface area6930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.240, 60.940, 48.180
Angle α, β, γ (deg.)90.00, 95.80, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.042378, 0.894002, -0.446055), (0.282521, 0.438957, 0.852935), (0.958325, -0.089875, -0.271176)16.6293, -14.77004, 7.59824
2given(-0.111306, 0.210137, 0.971315), (0.870401, 0.492297, -0.006763), (-0.479597, 0.844681, -0.237699)-2.48977, -9.23689, 19.9711
3given(-0.073613, 0.910422, -0.40708), (0.076187, 0.412128, 0.907935), (0.994372, 0.035821, -0.0997)15.6551, -15.77083, 4.70136
4given(-0.103506, 0.446346, 0.888854), (0.959385, 0.280588, -0.029181), (-0.262427, 0.849732, -0.45726)-1.16102, -7.9521, 23.93507
5given(-0.091159, 0.804272, -0.587228), (0.328155, 0.581008, 0.744811), (0.940215, -0.124806, -0.31689)21.85742, -12.0536, 7.97467
6given(-0.098254, 0.513685, 0.852334), (0.905666, 0.401129, -0.13735), (-0.412451, 0.758435, -0.50464)-0.01082, -6.10795, 26.95847
7given(-0.22724, 0.933342, -0.277911), (0.425039, 0.351817, 0.834006), (0.876187, 0.071397, -0.476654)13.37659, -13.8331, 11.09769
8given(0.157726, 0.227914, 0.960821), (0.860769, 0.445112, -0.246886), (-0.483941, 0.865986, -0.125976)-2.60638, -4.0892, 17.17687

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Components

#1: Protein/peptide
INSULIN /


Mass: 2383.698 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Tissue: PANCREAS / References: UniProt: P01315
#2: Protein/peptide
INSULIN /


Mass: 3403.927 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Tissue: PANCREAS / References: UniProt: P01315
#3: Chemical
ChemComp-IPH / PHENOL / Phenol


Mass: 94.111 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H6O
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 45 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorDetector: IMAGE PLATE / Date: May 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→10 Å / Num. obs: 11200 / % possible obs: 91 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.0625

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Processing

Software
NameVersionClassification
WEISdata collection
X-PLOR3.1model building
X-PLOR3.1refinement
WEISdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.5→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.206 --
obs0.206 11285 92 %
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2418 0 8 119 2545
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.858
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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