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- PDB-2f0a: Crystal Structure of Monomeric Uncomplexed form of Xenopus dishev... -

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Basic information

Entry
Database: PDB / ID: 2f0a
TitleCrystal Structure of Monomeric Uncomplexed form of Xenopus dishevelled PDZ domain
ComponentsSegment polarity protein dishevelled homolog DVL-2
KeywordsSIGNALING PROTEIN / dishevelled / PDZ domain / monomer
Function / homology
Function and homology information


convergent extension / convergent extension involved in gastrulation / ciliary basal body organization / establishment of planar polarity / syndecan binding / dorsal/ventral axis specification / activation of GTPase activity / gastrulation with mouth forming second / anterior/posterior axis specification / ciliary rootlet ...convergent extension / convergent extension involved in gastrulation / ciliary basal body organization / establishment of planar polarity / syndecan binding / dorsal/ventral axis specification / activation of GTPase activity / gastrulation with mouth forming second / anterior/posterior axis specification / ciliary rootlet / establishment or maintenance of cell polarity / cilium assembly / ephrin receptor signaling pathway / canonical Wnt signaling pathway / ephrin receptor binding / neurogenesis / neural tube closure / cell cortex / cytoplasmic vesicle / protein stabilization / intracellular signal transduction / cell surface / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Dishevelled-2 / Dishevelled protein domain / Dishevelled family / Dishevelled C-terminal / Dishevelled specific domain / Segment polarity protein dishevelled (Dsh) C terminal / Dishevelled-related protein / DIX domain / DIX domain superfamily / DIX domain ...Dishevelled-2 / Dishevelled protein domain / Dishevelled family / Dishevelled C-terminal / Dishevelled specific domain / Segment polarity protein dishevelled (Dsh) C terminal / Dishevelled-related protein / DIX domain / DIX domain superfamily / DIX domain / DIX domain profile. / Domain present in Dishevelled and axin / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Ubiquitin-like domain superfamily / Roll / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Mainly Beta
Similarity search - Domain/homology
: / Segment polarity protein dishevelled homolog DVL-2
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsFriedland, N. / Hung, L.-W. / Cheyette, B. / Moon, R.T. / Earnest, T.N.
CitationJournal: TO BE PUBLISHED
Title: Conformational flexibility in the PDZ domain of Dishevelled induced by target binding
Authors: Friedland, N. / Hung, L.-W. / Cheyette, B. / Miller, J.R. / Moon, R.T. / Earnest, T.N.
History
DepositionNov 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name
Revision 1.4Oct 16, 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_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_asym_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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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: Segment polarity protein dishevelled homolog DVL-2
B: Segment polarity protein dishevelled homolog DVL-2
C: Segment polarity protein dishevelled homolog DVL-2
D: Segment polarity protein dishevelled homolog DVL-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1666
Polymers44,0114
Non-polymers1552
Water2,738152
1
A: Segment polarity protein dishevelled homolog DVL-2


Theoretical massNumber of molelcules
Total (without water)11,0031
Polymers11,0031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Segment polarity protein dishevelled homolog DVL-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0622
Polymers11,0031
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Segment polarity protein dishevelled homolog DVL-2


Theoretical massNumber of molelcules
Total (without water)11,0031
Polymers11,0031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Segment polarity protein dishevelled homolog DVL-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0992
Polymers11,0031
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-47 kcal/mol
Surface area15790 Å2
MethodPISA
6
A: Segment polarity protein dishevelled homolog DVL-2

B: Segment polarity protein dishevelled homolog DVL-2
D: Segment polarity protein dishevelled homolog DVL-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1635
Polymers33,0083
Non-polymers1552
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation3_664-x+y+1,-x+1,z-1/31
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-35 kcal/mol
Surface area13730 Å2
MethodPISA
7
B: Segment polarity protein dishevelled homolog DVL-2
D: Segment polarity protein dishevelled homolog DVL-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1614
Polymers22,0062
Non-polymers1552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-18 kcal/mol
Surface area9790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.834, 89.834, 82.471
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
DetailsMonomeric form of dishevelled PDZ domain, uncomplexed

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Components

#1: Protein
Segment polarity protein dishevelled homolog DVL-2 / Dishevelled-2 / DSH homolog 2 / Xdsh


Mass: 11002.789 Da / Num. of mol.: 4 / Fragment: dishevelled PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: dvl2 / Plasmid: pET-21B / Production host: Escherichia coli (E. coli) / Strain (production host): N834(DE3) / References: UniProt: P51142
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.18 Å3/Da / Density % sol: 43.63 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 1.4 M ammonium sulfate 0.1 M sodium cacodylate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9798, 0.9801, 0.9611
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 1, 2002
RadiationMonochromator: Si(111) water-cooled / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97981
20.98011
30.96111
ReflectionResolution: 1.8→19.45 Å / Num. all: 34969 / Num. obs: 34969 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
Adxvdata processing
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→19.45 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.075 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.132
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25263 1753 5 %RANDOM
Rwork0.21371 ---
obs0.21571 33216 99.96 %-
all-34969 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.656 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2550 0 6 152 2708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222581
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6961.963486
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6245341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.31125.80693
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1915413
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.697155
X-RAY DIFFRACTIONr_chiral_restr0.1180.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021858
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2380.21186
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21756
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2149
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined00.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.95921765
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.60732743
X-RAY DIFFRACTIONr_scbond_it9.1116898
X-RAY DIFFRACTIONr_scangle_it11.2038743
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 135 -
Rwork0.301 2432 -
obs--99.88 %

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