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- PDB-5jyq: Structure of Conus Geographus insulin G1 -

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Basic information

Entry
Database: PDB / ID: 5jyq
TitleStructure of Conus Geographus insulin G1
Components
  • Insulin 1
  • Insulin 1b
KeywordsHORMONE / Venom Insulin
Function / homology
Function and homology information


hormone activity / glucose metabolic process / toxin activity / extracellular region
Similarity search - Function
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
Con-Ins G1b / Con-Ins G1a
Similarity search - Component
Biological speciesConus geographus (geography cone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLawrence, M.C. / Menting, J. / Norton, R.S. / Safavi-Hemami, H.
Funding support Australia, United States, 3items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1058233 Australia
European CommissionCONBIOS 330486
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM 48677 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: A minimized human insulin-receptor-binding motif revealed in a Conus geographus venom insulin.
Authors: Menting, J.G. / Gajewiak, J. / MacRaild, C.A. / Chou, D.H. / Disotuar, M.M. / Smith, N.A. / Miller, C. / Erchegyi, J. / Rivier, J.E. / Olivera, B.M. / Forbes, B.E. / Smith, B.J. / Norton, R. ...Authors: Menting, J.G. / Gajewiak, J. / MacRaild, C.A. / Chou, D.H. / Disotuar, M.M. / Smith, N.A. / Miller, C. / Erchegyi, J. / Rivier, J.E. / Olivera, B.M. / Forbes, B.E. / Smith, B.J. / Norton, R.S. / Safavi-Hemami, H. / Lawrence, M.C.
History
DepositionMay 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Sep 28, 2016Group: Database references
Revision 1.3Oct 19, 2016Group: Database references
Revision 1.4Sep 20, 2017Group: Author supporting evidence / Data collection / Derived calculations
Category: diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_special_symmetry / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Insulin 1
B: Insulin 1b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,2573
Polymers5,1612
Non-polymers961
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-15 kcal/mol
Surface area3400 Å2
MethodPISA
2
A: Insulin 1
B: Insulin 1b
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)42,05524
Polymers41,28616
Non-polymers7698
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation17_556x,z,-y+11
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation19_566-x,-z+1,-y+11
crystal symmetry operation20_565x,-z+1,y1
Buried area22500 Å2
ΔGint-365 kcal/mol
Surface area17490 Å2
MethodPISA
3
A: Insulin 1
B: Insulin 1b
hetero molecules

A: Insulin 1
B: Insulin 1b
hetero molecules

A: Insulin 1
B: Insulin 1b
hetero molecules

A: Insulin 1
B: Insulin 1b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,02712
Polymers20,6438
Non-polymers3844
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation17_556x,z,-y+11
crystal symmetry operation20_565x,-z+1,y1
Buried area9140 Å2
ΔGint-172 kcal/mol
Surface area10860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.910, 74.910, 74.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number207
Space group name H-MP432
Components on special symmetry positions
IDModelComponents
11A-101-

SO4

21A-208-

HOH

31B-112-

HOH

41B-113-

HOH

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Components

#1: Protein/peptide Insulin 1 /


Mass: 2358.720 Da / Num. of mol.: 1 / Fragment: residues 95-114 / Source method: obtained synthetically / Source: (synth.) Conus geographus (geography cone) / References: UniProt: A0A0B5AC95
#2: Protein/peptide Insulin 1b


Mass: 2802.083 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Conus geographus (geography cone) / References: UniProt: A0A0B5A8Q2
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 3.39 Å3/Da / Density % sol: 63.76 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop
Details: 2.0 M ammonium sulfate plus 10% DL-malate-MES-Tris (pH 9.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→37.455 Å / Num. obs: 5645 / % possible obs: 99 % / Redundancy: 8.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.368 / Net I/σ(I): 6.46
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 8.2 % / Rmerge(I) obs: 2.67 / Mean I/σ(I) obs: 0.9 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I3Z

3i3z


Resolution: 1.95→37.455 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.61
RfactorNum. reflection% reflection
Rfree0.233 283 5.01 %
Rwork0.2107 --
obs0.2118 5645 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→37.455 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms356 0 5 35 396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013371
X-RAY DIFFRACTIONf_angle_d1.392502
X-RAY DIFFRACTIONf_dihedral_angle_d26.2138
X-RAY DIFFRACTIONf_chiral_restr0.05249
X-RAY DIFFRACTIONf_plane_restr0.00664
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9505-2.03930.3071330.3434635X-RAY DIFFRACTION98
2.0393-2.14680.2945340.2972649X-RAY DIFFRACTION100
2.1468-2.28120.3055340.2464643X-RAY DIFFRACTION100
2.2812-2.45730.2189350.2412659X-RAY DIFFRACTION100
2.4573-2.70460.2554350.2331667X-RAY DIFFRACTION100
2.7046-3.09580.2136360.2027666X-RAY DIFFRACTION100
3.0958-3.89970.1787360.1693695X-RAY DIFFRACTION100
3.8997-37.46190.2392400.1806748X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 12.1088 Å / Origin y: 43.5354 Å / Origin z: 24.2004 Å
111213212223313233
T0.231 Å2-0.008 Å2-0.0012 Å2-0.2417 Å20.0026 Å2--0.256 Å2
L2.081 °20.689 °20.393 °2-2.0483 °20.8621 °2--1.9907 °2
S-0.0796 Å °0.0649 Å °0.0732 Å °-0.0071 Å °0.0338 Å °0.1124 Å °-0.0983 Å °-0.0461 Å °-0.0731 Å °
Refinement TLS groupSelection details: all

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