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- PDB-2z6e: Crystal Structure of Human DAAM1 FH2 -

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Basic information

Entry
Database: PDB / ID: 2z6e
TitleCrystal Structure of Human DAAM1 FH2
ComponentsDisheveled-associated activator of morphogenesis 1
KeywordsPROTEIN FIBRIL REGULATOR / coiled coil / Alternative splicing / Cytoplasm
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
Disheveled-associated activator of morphogenesis 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsYamashita, M. / Higashi, T. / Sato, Y. / Shirakawa, R. / Kita, T. / Horiuchi, H. / Fukai, S. / Nureki, O.
CitationJournal: Genes Cells / Year: 2007
Title: Crystal structure of human DAAM1 formin homology 2 domain
Authors: Yamashita, M. / Higashi, T. / Suetsugu, S. / Sato, Y. / Ikeda, T. / Shirakawa, R. / Kita, T. / Takenawa, T. / Horiuchi, H. / Fukai, S. / Nureki, O.
History
DepositionJul 31, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Disheveled-associated activator of morphogenesis 1
B: Disheveled-associated activator of morphogenesis 1
C: Disheveled-associated activator of morphogenesis 1
D: Disheveled-associated activator of morphogenesis 1


Theoretical massNumber of molelcules
Total (without water)193,2164
Polymers193,2164
Non-polymers00
Water2,198122
1
A: Disheveled-associated activator of morphogenesis 1
B: Disheveled-associated activator of morphogenesis 1


Theoretical massNumber of molelcules
Total (without water)96,6082
Polymers96,6082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9740 Å2
ΔGint-59 kcal/mol
Surface area41170 Å2
MethodPISA
2
C: Disheveled-associated activator of morphogenesis 1
D: Disheveled-associated activator of morphogenesis 1


Theoretical massNumber of molelcules
Total (without water)96,6082
Polymers96,6082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9710 Å2
ΔGint-58 kcal/mol
Surface area39780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.213, 91.895, 97.681
Angle α, β, γ (deg.)98.12, 90.32, 104.79
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Disheveled-associated activator of morphogenesis 1 / formin


Mass: 48303.957 Da / Num. of mol.: 4 / Fragment: FH2 domain, UNP residues 594-1012
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DAAM1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y4D1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 4000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU11
SYNCHROTRONSPring-8 BL41XU20.9793, 0.9795
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDSep 25, 2005
ADSC QUANTUM 3152CCDSep 25, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97931
30.97951
ReflectionResolution: 2.8→50 Å / Num. all: 49227 / Num. obs: 49227 / % possible obs: 87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 47.7 Å2 / Rsym value: 0.037 / Net I/σ(I): 16.5
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 1.9 / Rsym value: 0.184 / % possible all: 66

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCdata collection
DENZOdata reduction
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→29.82 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3368250.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.289 2469 5 %RANDOM
Rwork0.225 ---
obs0.225 49208 86.8 %-
all-49208 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.0029 Å2 / ksol: 0.278963 e/Å3
Displacement parametersBiso mean: 72.4 Å2
Baniso -1Baniso -2Baniso -3
1--10.35 Å216.41 Å25.52 Å2
2--26.63 Å216.3 Å2
3----16.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.82 Å0.76 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12628 0 0 122 12750
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d19.9
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it4.951.5
X-RAY DIFFRACTIONc_mcangle_it7.492
X-RAY DIFFRACTIONc_scbond_it6.932
X-RAY DIFFRACTIONc_scangle_it9.562.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.451 323 5 %
Rwork0.413 6094 -
obs--67.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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