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- PDB-1dph: CONFORMATIONAL CHANGES IN CUBIC INSULIN CRYSTALS IN THE PH RANGE 7-11 -

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Basic information

Entry
Database: PDB / ID: 1dph
TitleCONFORMATIONAL CHANGES IN CUBIC INSULIN CRYSTALS IN THE PH RANGE 7-11
Components
  • INSULIN A CHAIN (PH 11)
  • INSULIN B CHAIN (PH 11)
KeywordsHORMONE
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 / negative regulation of appetite / response to butyrate ...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 / 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 / negative regulation of lipid catabolic process / response to glucose / 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
1,2-DICHLOROETHANE / Insulin
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsGursky, O. / Badger, J. / Li, Y. / Caspar, D.L.D.
Citation
Journal: Biophys.J. / Year: 1992
Title: Conformational changes in cubic insulin crystals in the pH range 7-11.
Authors: Gursky, O. / Badger, J. / Li, Y. / Caspar, D.L.
#1: Journal: Biophys.J. / Year: 1992
Title: Monovalent Cation Binding in Cubic Insulin Crystals
Authors: Gursky, O. / Li, Y. / Badger, J. / Caspar, D.L.D.
#2: Journal: Biophys.J. / Year: 1992
Title: Flexibility in Crystalline Insulins
Authors: Badger, J.
#3: Journal: Acta Crystallogr.,Sect.B / Year: 1991
Title: Structure of the Pig Insulin Dimer in the Cubic Crystal
Authors: Badger, J. / Harris, M.R. / Reynolds, C.D. / Evans, A.C. / Dodson, E.J. / Dodson, G.G. / North, A.C.T.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991
Title: Water Structure in Cubic Insulin Crystals
Authors: Badger, J. / Caspar, D.L.D.
#5: Journal: J.Mol.Biol. / Year: 1978
Title: Zinc-Free Cubic Pig Insulin: Crystallization and Structure Determination
Authors: Dodson, E.J. / Dodson, G.G. / Lewitova, A. / Sabesan, M.
History
DepositionOct 30, 1992Processing site: BNL
Revision 1.0Jan 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET THERE IS A SHEET COMPRISING TWO ANTIPARALLEL STRANDS PHE B 24 - TYR B 26 FROM TWO DIMER- ...SHEET THERE IS A SHEET COMPRISING TWO ANTIPARALLEL STRANDS PHE B 24 - TYR B 26 FROM TWO DIMER-FORMING INSULIN MOLECULES.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INSULIN A CHAIN (PH 11)
B: INSULIN B CHAIN (PH 11)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8664
Polymers5,7442
Non-polymers1222
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-20 kcal/mol
Surface area3270 Å2
MethodPISA
2
A: INSULIN A CHAIN (PH 11)
B: INSULIN B CHAIN (PH 11)
hetero molecules

A: INSULIN A CHAIN (PH 11)
B: INSULIN B CHAIN (PH 11)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7318
Polymers11,4874
Non-polymers2444
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_565x,-y+1,-z+1/21
Buried area4900 Å2
ΔGint-72 kcal/mol
Surface area5350 Å2
MethodPISA
3
A: INSULIN A CHAIN (PH 11)
hetero molecules

A: INSULIN A CHAIN (PH 11)
hetero molecules

B: INSULIN B CHAIN (PH 11)
hetero molecules

B: INSULIN B CHAIN (PH 11)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7318
Polymers11,4874
Non-polymers2444
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_556-x+1/2,y,-z+11
crystal symmetry operation5_555z,x,y1
crystal symmetry operation20_556-z+1/2,x,-y+11
Buried area3170 Å2
ΔGint-66 kcal/mol
Surface area7080 Å2
MethodPISA
4
A: INSULIN A CHAIN (PH 11)
B: INSULIN B CHAIN (PH 11)
hetero molecules

A: INSULIN A CHAIN (PH 11)
B: INSULIN B CHAIN (PH 11)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7318
Polymers11,4874
Non-polymers2444
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_556-x+1/2,y,-z+11
Buried area4240 Å2
ΔGint-54 kcal/mol
Surface area5570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.900, 78.900, 78.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11B-230-

HOH

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Components

#1: Protein/peptide INSULIN A CHAIN (PH 11)


Mass: 2339.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P01317
#2: Protein/peptide INSULIN B CHAIN (PH 11)


Mass: 3403.927 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P01317
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-DCE / 1,2-DICHLOROETHANE / ETHYLENE DICHLORIDE


Mass: 98.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4Cl2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE 1,2-DICHLOROETHANE IS BOUND IS CIS CONFORMATION IN A SYMMETRIC POSITION ACROSS THE ...THE 1,2-DICHLOROETHANE IS BOUND IS CIS CONFORMATION IN A SYMMETRIC POSITION ACROSS THE CRYSTALLOGRAPHIC TWO-FOLD AXIS BETWEEN THE TWO INSULIN DIMER-FORMING MOLECULES.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.56 Å3/Da / Density % sol: 65.47 %
Crystal grow
*PLUS
pH: 9.2 / Method: microdialysis
Details: referred to 'Dodson, E.J.', (1978) J.Mol.Biol., 125, 387-396
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein11
20.2 M12Na2HPO4
30.01 MNa3EDTA11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. obs: 5588 / % possible obs: 90 % / Num. measured all: 21417 / Rmerge(I) obs: 0.069

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.19 / Highest resolution: 1.9 Å
Details: IN 1BPH AND 1CPH, THE SIDE CHAIN OF GLU A 4 CAN ADOPT TWO ALTERNATIVE POSITIONS WHICH OVERLAP. THEIR RELATIVE WEIGHT AND THE ATOMIC POSITIONS OF THE SECOND CONFORMER ARE NOT ACCURATELY ...Details: IN 1BPH AND 1CPH, THE SIDE CHAIN OF GLU A 4 CAN ADOPT TWO ALTERNATIVE POSITIONS WHICH OVERLAP. THEIR RELATIVE WEIGHT AND THE ATOMIC POSITIONS OF THE SECOND CONFORMER ARE NOT ACCURATELY DETERMINED. IN 1APH, 1BPH, AND 1DPH, THE SIDE CHAIN OF GLU B 21 IS DISORDERED. IT HAS BEEN MODELED AS SUPERPOSITION OF TWO CONFORMATIONS BUT ATOMIC POSITIONS FOR THESE CONFORMATIONS ARE PROBABLY NOT VERY ACCURATE. THE SIDE CHAIN OF LYS B 29 IS POORLY DEFINED IN THE ELECTRON DENSITY MAPS. IN 1APH AND 1CPH, IT IS INCLUDED WITH PARTIAL OCCUPANCY. IN 1BPH AND 1DPH, ITS COORDINATES HAVE BEEN OMITTED FROM THE ENTRY. THE MAIN AND SIDE CHAIN OF ALA B 30 (C-TERMINAL RESIDUE OF CHAIN B) CAN ADOPT TWO SEPARATE CONFORMATIONS AND IS DISORDERED IN EACH OF THESE CONFORMATIONS, WHICH LIMITED THE ACCURACY OF DETERMINATION OF ATOMIC POSITIONS FOR THE CONFORMERS OF ALA B 30. IN 1APH AND 1CPH, SINGLE ALTERNATIVE CONFORMERS ARE PREDOMINANT BUT, DUE TO DISORDER, THEY ARE ASSIGNED PARTIAL OCCUPANCIES. IN 1BPH AND 1DPH, BOTH ALTERNATIVE CONFORMERS ARE INCLUDED IN THE ENTRY.
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms439 0 5 60 504
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.9 Å / Rfactor obs: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_angle_d / Dev ideal: 0.053

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