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- PDB-4krr: Crystal structure of Drosophila WntD N-terminal domain-linker (re... -

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Basic information

Entry
Database: PDB / ID: 4krr
TitleCrystal structure of Drosophila WntD N-terminal domain-linker (residues 31-240)
ComponentsWnt inhibitor of Dorsal protein
KeywordsSIGNALING PROTEIN / WntD / uncomplexed Wnt / N-terminal domain / linker / WNT / growth factor / WNT signaling / extracellular
Function / homology
Function and homology information


ventral furrow formation / WNT ligand biogenesis and trafficking / non-canonical Wnt signaling pathway / germ cell migration / frizzled binding / regulation of embryonic development / cell fate commitment / canonical Wnt signaling pathway / extracellular matrix / cytokine activity ...ventral furrow formation / WNT ligand biogenesis and trafficking / non-canonical Wnt signaling pathway / germ cell migration / frizzled binding / regulation of embryonic development / cell fate commitment / canonical Wnt signaling pathway / extracellular matrix / cytokine activity / neuron differentiation / defense response to Gram-positive bacterium / extracellular space / extracellular region
Similarity search - Function
Wnt / Wnt, C-terminal domain / wnt family / found in Wnt-1
Similarity search - Domain/homology
Wnt inhibitor of Dorsal protein
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.124 Å
AuthorsChu, M.L.-H. / Choi, H.-J. / Ahn, V.E. / Daniels, D.L. / Nusse, R. / Weis, W.I.
CitationJournal: Structure / Year: 2013
Title: Structural Studies of Wnts and Identification of an LRP6 Binding Site.
Authors: Chu, M.L. / Ahn, V.E. / Choi, H.J. / Daniels, D.L. / Nusse, R. / Weis, W.I.
History
DepositionMay 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Wnt inhibitor of Dorsal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9216
Polymers24,5291
Non-polymers3915
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.625, 59.625, 66.955
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Wnt inhibitor of Dorsal protein / Protein Wnt-8 / dWnt-8


Mass: 24529.408 Da / Num. of mol.: 1 / Fragment: N-terminal domain-linker
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG8458, Wnt8, wntD / Plasmid: pMT/BiP/V5-His A / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 / References: UniProt: Q9VFX1
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.43 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% PEG 1000, 0.1M Bis-Tris, 0.2M magnesium chloride, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 28, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.124→59.625 Å / Num. all: 13310 / Num. obs: 13301 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Redundancy: 13.5 % / Rsym value: 0.076 / Net I/σ(I): 23.2
Reflection shell

Rmerge(I) obs: 0.016 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.124-2.2413.80.52641819151.58399.9
2.24-2.3713.50.82460518280.969100
2.37-2.5412.81.32192117150.57899.8
2.54-2.74142.22267216160.352100
2.74-313.94.22047514780.179100
3-3.3612.97.81727213400.09599.8
3.36-3.8813.914.51641211780.049100
3.88-4.7512.8191292410100.03599.8
4.75-6.7213.718.3107997870.03499.9
6.72-29.81312.922.655924340.02398.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å14.91 Å
Translation3.5 Å14.91 Å
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
5-500.010.8980.8911047
3.97-50.9841.0251036
3.47-3.970.971.0231021
3.15-3.470.9610.971026
2.92-3.150.9350.9291015
2.75-2.920.9170.8931030
2.61-2.750.8960.8491005
2.5-2.610.8880.8391015

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
PHASER2.3.0phasing
CNSrefinement
SCALA3.3.16data scaling
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4F0A

4f0a


Resolution: 2.124→29.812 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8246 / SU ML: 0.21 / σ(F): 0 / Phase error: 24.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2035 654 4.93 %RANDOM
Rwork0.1793 ---
obs0.1805 13272 99.74 %-
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 142.29 Å2 / Biso mean: 55.412 Å2 / Biso min: 25.17 Å2
Refinement stepCycle: LAST / Resolution: 2.124→29.812 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1465 0 25 72 1562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021517
X-RAY DIFFRACTIONf_angle_d0.5612038
X-RAY DIFFRACTIONf_chiral_restr0.039220
X-RAY DIFFRACTIONf_plane_restr0.002269
X-RAY DIFFRACTIONf_dihedral_angle_d12.422557
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.124-2.2880.27251410.246925032644
2.288-2.51810.25391230.21425012624
2.5181-2.88220.27051440.202725132657
2.8822-3.63030.21911210.185625272648
3.6303-29.81540.16391250.157925742699
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)
18.4225-6.22373.85925.1259-3.59685.27770.11440.90170.2246-1.10320.1442-0.911-0.05291.0614-0.2520.5093-0.1928-0.00680.6503-0.09130.573515.6549-17.0325-6.8124
24.2225-0.8365-0.76134.93971.23063.9457-0.12520.1784-0.04930.00130.3485-0.27960.06190.5269-0.20270.2676-0.0674-0.09540.3763-0.01550.2229.7044-19.965-3.1144
35.2516-2.9131-5.28066.32316.41468.9067-0.17740.406-0.5397-0.03830.0492-0.20950.30680.4180.11670.29340.0235-0.12140.4035-0.040.3889.0875-32.4588-15.3606
45.3643-0.4024-1.86133.1777-0.31845.8328-0.32710.0954-0.0328-0.05530.14390.4196-0.2891-0.28190.14510.3013-0.0104-0.10370.23190.05010.3236-4.4307-17.95560.2185
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 54 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 140 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 141 through 185 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 186 through 232 )A0

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