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- PDB-2wfv: Crystal structure of DILP5 variant C4 -

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Basic information

Entry
Database: PDB / ID: 2wfv
TitleCrystal structure of DILP5 variant C4
Components
  • PROBABLE INSULIN-LIKE PEPTIDE 5 A CHAIN
  • PROBABLE INSULIN-LIKE PEPTIDE 5 B CHAIN
KeywordsSIGNALING PROTEIN / CLEAVAGE ON PAIR OF BASIC RESIDUES
Function / homology
Function and homology information


negative regulation of entry into reproductive diapause / Insulin signaling pathway / female mating behavior / carbohydrate homeostasis / sleep / locomotory behavior / insulin receptor binding / hormone activity / insulin receptor signaling pathway / receptor ligand activity ...negative regulation of entry into reproductive diapause / Insulin signaling pathway / female mating behavior / carbohydrate homeostasis / sleep / locomotory behavior / insulin receptor binding / hormone activity / insulin receptor signaling pathway / receptor ligand activity / extracellular space / extracellular region
Similarity search - Function
Insulin-related peptide, invertebrates / 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
Probable insulin-like peptide 5
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.85 Å
AuthorsKulahin, N. / Schluckebier, G. / Sajid, W. / De Meyts, P.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural and Biological Properties of the Drosophila Insulin-Like Peptide 5 Show Evolutionary Conservation.
Authors: Sajid, W. / Kulahin, N. / Schluckebier, G. / Ribel, U. / Henderson, H.R. / Tatar, M. / Hansen, B.F. / Svendsen, A.M. / Kiselyov, V.V. / Norgaard, P. / Wahlund, P. / Brandt, J. / Kohanski, R. ...Authors: Sajid, W. / Kulahin, N. / Schluckebier, G. / Ribel, U. / Henderson, H.R. / Tatar, M. / Hansen, B.F. / Svendsen, A.M. / Kiselyov, V.V. / Norgaard, P. / Wahlund, P. / Brandt, J. / Kohanski, R.A. / Andersen, A.S. / De Meyts, P.
History
DepositionApr 15, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 18, 2012Group: Other
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROBABLE INSULIN-LIKE PEPTIDE 5 A CHAIN
B: PROBABLE INSULIN-LIKE PEPTIDE 5 B CHAIN


Theoretical massNumber of molelcules
Total (without water)5,2482
Polymers5,2482
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-11.3 kcal/mol
Surface area3270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.445, 40.445, 45.241
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein/peptide PROBABLE INSULIN-LIKE PEPTIDE 5 A CHAIN / INSULIN-RELATED PEPTIDE / DILP5 / DROSOPHILA INSULIN-LIKE PEPTIDE 5


Mass: 2795.097 Da / Num. of mol.: 1 / Fragment: RESIDUES 84-108 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q7KUD5
#2: Protein/peptide PROBABLE INSULIN-LIKE PEPTIDE 5 B CHAIN / INSULIN-RELATED PEPTIDE / DILP5 / DROSOPHILA INSULIN-LIKE PEPTIDE 5


Mass: 2452.898 Da / Num. of mol.: 1 / Fragment: RESIDUES 24-46
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q7KUD5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 95 TO ASN
Has protein modificationY
Sequence detailsLYS12A HAS BEEN MUTATED TO ASN12A AS A PART OF CLONING STRATEGY

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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: 1.59 Å3/Da / Density % sol: 23 % / Description: NONE
Crystal growDetails: 20% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: CCD / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→24.18 Å / Num. obs: 3164 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 12.8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 56
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.54 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 1.85→24.18 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.179 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.232 329 9.4 %RANDOM
Rwork0.199 ---
obs0.202 3164 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.85→24.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms340 0 0 23 363
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021364
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.98495
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.948550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.66421.87516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.5971561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.025155
X-RAY DIFFRACTIONr_chiral_restr0.0950.255
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02279
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.2145
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.2253
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.211
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.231
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3440.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9181.5243
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3722379
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7293132
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8934.5113
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 23 -
Rwork0.222 224 -
obs--99.6 %
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)
15.89130.5091.44059.33724.27056.0474-0.16530.09080.2106-0.42340.2872-0.4032-0.40190.1105-0.1219-0.0847-0.0146-0.0027-0.1036-0.017-0.111811.92912.241312.5329
26.9443-1.71661.92435.09223.19246.9139-0.25690.29490.4605-0.54720.0109-0.1218-0.4912-0.13060.246-0.0078-0.035-0.0256-0.0640.0083-0.06025.76751.31858.357
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 25
2X-RAY DIFFRACTION2B1 - 23

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