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- PDB-2j1d: Crystallization of hDaam1 C-terminal Fragment -

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Basic information

Entry
Database: PDB / ID: 2j1d
TitleCrystallization of hDaam1 C-terminal Fragment
ComponentsDISHEVELED-ASSOCIATED ACTIVATOR OF MORPHOGENESIS 1
KeywordsPROTEIN BINDING / ACTIN ASSEMBLY
Function / homology
Function and homology information


PCP/CE pathway / motile cilium / Wnt signaling pathway, planar cell polarity pathway / RHOB GTPase cycle / RHOC GTPase cycle / CDC42 GTPase cycle / RHOA GTPase cycle / stress fiber / ciliary basal body / RHO GTPases Activate Formins ...PCP/CE pathway / motile cilium / Wnt signaling pathway, planar cell polarity pathway / RHOB GTPase cycle / RHOC GTPase cycle / CDC42 GTPase cycle / RHOA GTPase cycle / stress fiber / ciliary basal body / RHO GTPases Activate Formins / small GTPase binding / actin binding / actin cytoskeleton organization / perinuclear region of cytoplasm / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Formin, FH2 domain / Diaphanous autoregulatory (DAD) domain / Diaphanous autoregulatory domain (DAD) profile. / Formin, FH3 domain / Formin, GTPase-binding domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain ...Formin, FH2 domain / Diaphanous autoregulatory (DAD) domain / Diaphanous autoregulatory domain (DAD) profile. / Formin, FH3 domain / Formin, GTPase-binding domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain profile. / Formin, FH2 domain / Formin, FH2 domain superfamily / Formin Homology 2 Domain / Formin homology-2 (FH2) domain profile. / Formin Homology 2 Domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Armadillo-like helical / Armadillo-type fold / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Disheveled-associated activator of morphogenesis 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.25 Å
AuthorsLu, J. / Meng, W. / Poy, F. / Eck, M.J.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structure of the Fh2 Domain of Daam1: Implications for Formin Regulation of Actin Assembly.
Authors: Lu, J. / Meng, W. / Poy, F. / Maiti, S. / Goode, B.L. / Eck, M.J.
History
DepositionAug 10, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: DISHEVELED-ASSOCIATED ACTIVATOR OF MORPHOGENESIS 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1903
Polymers56,0031
Non-polymers1872
Water1,35175
1
G: DISHEVELED-ASSOCIATED ACTIVATOR OF MORPHOGENESIS 1
hetero molecules

G: DISHEVELED-ASSOCIATED ACTIVATOR OF MORPHOGENESIS 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,3796
Polymers112,0052
Non-polymers3744
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area10540 Å2
ΔGint-64.3 kcal/mol
Surface area41870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.897, 100.343, 148.397
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein DISHEVELED-ASSOCIATED ACTIVATOR OF MORPHOGENESIS 1 / DAAM1


Mass: 56002.605 Da / Num. of mol.: 1 / Fragment: FH2 DOMAIN, RESIDUES 596-1078
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y4D1
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 4.19 Å3/Da / Density % sol: 70.42 %
Crystal growpH: 6.2 / Details: pH 6.20

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.008
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 12, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 2.55→20 Å / Num. obs: 24546 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.25→19.83 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.932 / SU B: 12.221 / SU ML: 0.156 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.283 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1500 6 %RANDOM
Rwork0.218 ---
obs0.22 23499 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.76 Å2
Baniso -1Baniso -2Baniso -3
1--6.26 Å20 Å20 Å2
2--11.9 Å20 Å2
3----5.63 Å2
Refinement stepCycle: LAST / Resolution: 2.25→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3202 0 11 75 3288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223259
X-RAY DIFFRACTIONr_bond_other_d0.0060.022324
X-RAY DIFFRACTIONr_angle_refined_deg1.3071.984369
X-RAY DIFFRACTIONr_angle_other_deg0.90135683
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2155393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.35325.215163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.89115654
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4281521
X-RAY DIFFRACTIONr_chiral_restr0.0740.2480
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023553
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02622
X-RAY DIFFRACTIONr_nbd_refined0.1970.2737
X-RAY DIFFRACTIONr_nbd_other0.1880.22269
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21596
X-RAY DIFFRACTIONr_nbtor_other0.0890.21733
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.278
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2050.2100
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5520.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8921.52594
X-RAY DIFFRACTIONr_mcbond_other0.0571.5790
X-RAY DIFFRACTIONr_mcangle_it0.82423177
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.39831485
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0174.51192
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: 2.25→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 18 -
Rwork0.242 296 -
obs--100 %
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)
14.77532.60431.66833.28710.72637.0474-0.37240.60530.6948-0.2309-0.04640.1702-0.5325-0.35410.4189-0.42280.1524-0.05610.0826-0.0405-0.229949.337132.788-41.1394
23.129-0.5539-1.18721.70650.08024.5541-0.14560.001-0.0609-0.02690.0008-0.24170.12-0.06720.1449-0.1581-0.0118-0.0333-0.0078-0.0261-0.124327.865923.5711-28.0768
31.1357-0.28161.8730.1488-0.18824.3836-0.1423-0.01950.0507-0.079-0.1542-0.0134-0.3064-0.10290.2965-0.0915-0.0019-0.03520.0062-0.0151-0.113233.852731.609713.7391
41.0953-1.16430.45765.9466-5.81818.2794-0.2444-0.2491-0.4278-0.27190.2892-0.02590.9938-0.2597-0.04480.1218-0.0161-0.03050.12160.14340.157242.54528.826841.6079
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1G601 - 653
2X-RAY DIFFRACTION2G683 - 768
3X-RAY DIFFRACTION3G769 - 961
4X-RAY DIFFRACTION4G962 - 1024

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