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- PDB-3e07: Crystal structure of spatzle cystine knot -

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Basic information

Entry
Database: PDB / ID: 30000000
TitleCrystal structure of spatzle cystine knot
ComponentsProtein spaetzle
KeywordsCYTOKINE / cystine knot / Toll ligand / Antimicrobial / Developmental protein / Fungicide / Glycoprotein / Secreted
Function / homology
Function and homology information


positive regulation of antimicrobial peptide biosynthetic process / positive regulation of antifungal peptide biosynthetic process / response to tumor cell / Formation of the trans-membrane 'signalling complex' / Adaptor protein complex binds to TL receptor at the plasma membrane / DL and DIF homodimers bind to TUB and phosphorylated PLL in the TL receptor 'signalling complex' / DL and DIF homodimers complexed with CACT are all phosphorylated in the TL receptor 'signalling complex' / Activated PLL kinase is autophosphorylated in the TL receptor 'signalling complex' / Phosphorylated CACT, DL and DIF homodimers dissociate from the TL receptor 'signalling complex' / PLL kinase binds to TUB in the TL receptor 'signalling complex' ...positive regulation of antimicrobial peptide biosynthetic process / positive regulation of antifungal peptide biosynthetic process / response to tumor cell / Formation of the trans-membrane 'signalling complex' / Adaptor protein complex binds to TL receptor at the plasma membrane / DL and DIF homodimers bind to TUB and phosphorylated PLL in the TL receptor 'signalling complex' / DL and DIF homodimers complexed with CACT are all phosphorylated in the TL receptor 'signalling complex' / Activated PLL kinase is autophosphorylated in the TL receptor 'signalling complex' / Phosphorylated CACT, DL and DIF homodimers dissociate from the TL receptor 'signalling complex' / PLL kinase binds to TUB in the TL receptor 'signalling complex' / positive regulation of antifungal peptide production / positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria / Toll binding / central nervous system formation / oocyte dorsal/ventral axis specification / cell competition in a multicellular organism / larval somatic muscle development / positive regulation of antimicrobial peptide production / antifungal innate immune response / Toll signaling pathway / dorsal/ventral axis specification / dorsal/ventral pattern formation / motor neuron axon guidance / defense response to fungus / cytokine activity / growth factor activity / response to hydrogen peroxide / response to wounding / killing of cells of another organism / defense response to Gram-negative bacterium / negative regulation of neuron apoptotic process / receptor ligand activity / defense response to Gram-positive bacterium / innate immune response / positive regulation of gene expression / protein homodimerization activity / extracellular space / extracellular region
Similarity search - Function
Spaetzle / Spaetzle / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsHoffmann, A. / Funkner, A. / Neumann, P. / Juhnke, S. / Walther, M. / Schierhorn, A. / Weininger, U. / Balbach, J. / Reuter, G. / Stubbs, M.T.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Biophysical Characterization of Refolded Drosophila Spatzle, a Cystine Knot Protein, Reveals Distinct Properties of Three Isoforms
Authors: Hoffmann, A. / Funkner, A. / Neumann, P. / Juhnke, S. / Walther, M. / Schierhorn, A. / Weininger, U. / Balbach, J. / Reuter, G. / Stubbs, M.T.
History
DepositionJul 31, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / 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_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein spaetzle
B: Protein spaetzle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1053
Polymers26,0132
Non-polymers921
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-14 kcal/mol
Surface area11610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.800, 58.980, 62.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A,B, using restrain
22chain A,B, using restrain
33chain A,B, using restrain
44chain A,B, using restrain

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PHEPHETYRTYRAA8 - 188 - 18
121LYSLYSGLUGLUAA39 - 4839 - 48
131PROPROPHEPHEAA53 - 5653 - 56
141ASNASNGLNGLNAA65 - 9065 - 90
151LYSLYSCYSCYSAA94 - 9894 - 98
161CYSCYSLEULEUAA99 - 10399 - 103
171PHEPHETYRTYRBB8 - 188 - 18
181LYSLYSGLUGLUBB39 - 4839 - 48
191PROPROPHEPHEBB53 - 5653 - 56
1101ASNASNGLNGLNBB65 - 9065 - 90
1111LYSLYSCYSCYSBB94 - 9894 - 98
1121CYSCYSLEULEUBB99 - 10399 - 103
212PHEPHECYSCYSAA8 - 108 - 10
222SERSERSERSERAA1212
232ARGARGTYRTYRAA14 - 1814 - 18
242ALAALACYSCYSAA41 - 4741 - 47
252CYSCYSPHEPHEAA54 - 5654 - 56
262ASNASNCYSCYSAA65 - 6865 - 68
272GLNGLNGLNGLNAA70 - 7470 - 74
282THRTHRILEILEAA76 - 8076 - 80
292SERSERGLYGLYAA82 - 8482 - 84
2102LEULEUASPASPAA86 - 8786 - 87
2112VALVALGLNGLNAA88 - 9088 - 90
2122LYSLYSSERSERAA94 - 9794 - 97
2132CYSCYSLEULEUAA99 - 10399 - 103
2142PHEPHECYSCYSBB8 - 108 - 10
2152SERSERSERSERBB1212
2162ARGARGTYRTYRBB14 - 1814 - 18
2172ALAALACYSCYSBB41 - 4741 - 47
2182CYSCYSPHEPHEBB54 - 5654 - 56
2192ASNASNCYSCYSBB65 - 6865 - 68
2202GLNGLNGLNGLNBB70 - 7470 - 74
2212THRTHRILEILEBB76 - 8076 - 80
2222SERSERGLYGLYBB82 - 8482 - 84
2232LEULEUASPASPBB86 - 8786 - 87
2242VALVALGLNGLNBB88 - 9088 - 90
2252LYSLYSSERSERBB94 - 9794 - 97
2262CYSCYSLEULEUBB99 - 10399 - 103
313GLUGLUGLYGLYAA48 - 4948 - 49
323ALAALATYRTYRAA57 - 6457 - 64
333GLUGLUGLYGLYBB48 - 4948 - 49
343ALAALATYRTYRBB57 - 6457 - 64
414ALAALATYRTYRAA57 - 6457 - 64
424ALAALATYRTYRBB57 - 6457 - 64

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein Protein spaetzle / Protein spaetzle C-106 / Spatzle Isoform Spz11.7


Mass: 13006.618 Da / Num. of mol.: 2 / Fragment: Spatzle cystine knot, Protein spaetzle C-106
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Strain: Oregon R / Gene: spz / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: P48607
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 1.86 Å3/Da / Density % sol: 33.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50mM TRIS/HCl, 20% PEG 3350, 10mM betaine monohydrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 13, 2008 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 7988 / Num. obs: 7919 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Redundancy: 4.712 % / Biso Wilson estimate: 59.222 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.062 / Net I/σ(I): 16.49
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 4.88 % / Rmerge(I) obs: 0.631 / Mean I/σ(I) obs: 2.5 / Num. measured obs: 4327 / Num. unique all: 886 / Num. unique obs: 886 / Rsym value: 0.706 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 60.58 / Packing: 0

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
CNS1.2refinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1BTG, 1SG1, 1BET, 1SGF

1btg

1sg1

1bet

1sgf


Resolution: 2.4→19.83 Å / Rfactor Rfree error: 0.011 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.746 / Data cutoff high absF: 1116162 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.265 610 7.7 %RANDOM
Rwork0.222 ---
all-7988 --
obs-7919 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.475 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso max: 152.93 Å2 / Biso mean: 64.958 Å2 / Biso min: 21.89 Å2
Baniso -1Baniso -2Baniso -3
1--8.8 Å20 Å20 Å2
2---3.12 Å20 Å2
3---11.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.62 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1417 0 6 37 1460
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d27.3
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_mcbond_it6.861.5
X-RAY DIFFRACTIONc_mcangle_it9.62
X-RAY DIFFRACTIONc_scbond_it8.252
X-RAY DIFFRACTIONc_scangle_it122.5
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDRmsTypeWeight
11BX-RAY DIFFRACTION0.613restrain0
22BX-RAY DIFFRACTION1.09restrain0
33BX-RAY DIFFRACTION0.922restrain0
44BX-RAY DIFFRACTION1.661restrain0
LS refinement shellResolution: 2.4→2.47 Å / Rfactor Rfree error: 0.068 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.46 47 7.3 %
Rwork0.371 595 -
all-642 -
obs--99.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4ecpox-tpp-fad.paramecpox-tpp-fad.top

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