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- PDB-3a8q: Low-resolution crystal structure of the Tiam2 PHCCEx domain -

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Basic information

Entry
Database: PDB / ID: 3a8q
TitleLow-resolution crystal structure of the Tiam2 PHCCEx domain
ComponentsT-lymphoma invasion and metastasis-inducing protein 2
KeywordsSIGNALING PROTEIN / guanine nucleotide exchange factor / Alternative splicing / Cell projection / Coiled coil / Cytoplasm / Guanine-nucleotide releasing factor / Lipoprotein / Myristate / Phosphoprotein
Function / homology
Function and homology information


NRAGE signals death through JNK / RAC1 GTPase cycle / G alpha (12/13) signalling events / small GTPase-mediated signal transduction / positive regulation of axonogenesis / GTPase activator activity / guanyl-nucleotide exchange factor activity / filopodium / lamellipodium / growth cone ...NRAGE signals death through JNK / RAC1 GTPase cycle / G alpha (12/13) signalling events / small GTPase-mediated signal transduction / positive regulation of axonogenesis / GTPase activator activity / guanyl-nucleotide exchange factor activity / filopodium / lamellipodium / growth cone / perikaryon / synapse / membrane / cytoplasm
Similarity search - Function
Helix Hairpins - #680 / TIAM1, CC-Ex domain / Tiam1/Tiam2/Protein still life / T-lymphoma invasion and metastasis CC-Ex domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Dbl homology (DH) domain superfamily ...Helix Hairpins - #680 / TIAM1, CC-Ex domain / Tiam1/Tiam2/Protein still life / T-lymphoma invasion and metastasis CC-Ex domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Helix Hairpins / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / Helix non-globular / PDZ domain / PDZ superfamily / Special / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Rho guanine nucleotide exchange factor TIAM2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.2 Å
AuthorsTerawaki, S. / Kitano, K. / Mori, T. / Zhai, Y. / Higuchi, Y. / Itoh, N. / Watanabe, T. / Kaibuchi, K. / Hakoshima, T.
CitationJournal: Embo J. / Year: 2010
Title: The PHCCEx domain of Tiam1/2 is a novel protein- and membrane-binding module
Authors: Terawaki, S. / Kitano, K. / Mori, T. / Zhai, Y. / Higuchi, Y. / Itoh, N. / Watanabe, T. / Kaibuchi, K. / Hakoshima, T.
History
DepositionOct 7, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2009Provider: 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 ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T-lymphoma invasion and metastasis-inducing protein 2
B: T-lymphoma invasion and metastasis-inducing protein 2
C: T-lymphoma invasion and metastasis-inducing protein 2
D: T-lymphoma invasion and metastasis-inducing protein 2


Theoretical massNumber of molelcules
Total (without water)119,7034
Polymers119,7034
Non-polymers00
Water0
1
A: T-lymphoma invasion and metastasis-inducing protein 2


Theoretical massNumber of molelcules
Total (without water)29,9261
Polymers29,9261
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: T-lymphoma invasion and metastasis-inducing protein 2


Theoretical massNumber of molelcules
Total (without water)29,9261
Polymers29,9261
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: T-lymphoma invasion and metastasis-inducing protein 2


Theoretical massNumber of molelcules
Total (without water)29,9261
Polymers29,9261
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: T-lymphoma invasion and metastasis-inducing protein 2


Theoretical massNumber of molelcules
Total (without water)29,9261
Polymers29,9261
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.560, 105.560, 287.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
T-lymphoma invasion and metastasis-inducing protein 2 / TIAM-2 / SIF and TIAM1-like exchange factor


Mass: 29925.717 Da / Num. of mol.: 4 / Fragment: PHCCEx domain, residues 500-757
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tiam2, Kiaa2016, Stef / Plasmid: pGEX6P-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21RIL / References: UniProt: Q6ZPF3

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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: 3.35 Å3/Da / Density % sol: 63.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% PEG 3350, 100mM bis-tris pH 6.5, 200mM Lithium sulfate monohydorate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 25, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 27986 / % possible obs: 91.7 % / Redundancy: 13.1 %
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 9.5 % / Mean I/σ(I) obs: 2 / % possible all: 52.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
CNS1.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 3.2→45.56 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 4378236.59 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.332 2518 9.9 %RANDOM
Rwork0.283 ---
obs0.283 25490 91.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 91.4106 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 144.4 Å2
Baniso -1Baniso -2Baniso -3
1-27.32 Å20 Å20 Å2
2--27.32 Å20 Å2
3----54.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.73 Å0.62 Å
Luzzati d res low-5 Å
Luzzati sigma a1.08 Å1.02 Å
Refinement stepCycle: LAST / Resolution: 3.2→45.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7412 0 0 0 7412
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.488 255 9.5 %
Rwork0.454 2419 -
obs--59.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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