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- PDB-3kzd: Crystal Structure of Free T-cell Lymphoma Invasion and Metastasis... -

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Basic information

Entry
Database: PDB / ID: 3kzd
TitleCrystal Structure of Free T-cell Lymphoma Invasion and Metastasis-1 PDZ Domain
ComponentsT-lymphoma invasion and metastasis-inducing protein 1
KeywordsSIGNALING PROTEIN / PDZ / CELL JUNCTION / CELL ADHESION / TIAM1 / Guanine nucleotide exchange factor / Guanine-nucleotide releasing factor / Lipoprotein / Myristate / Phosphoprotein / Polymorphism
Function / homology
Function and homology information


positive regulation of Schwann cell chemotaxis / regulation of non-canonical Wnt signaling pathway / regulation of dopaminergic neuron differentiation / extrinsic component of postsynaptic density membrane / Activated NTRK2 signals through CDK5 / regulation of epithelial to mesenchymal transition / positive regulation of dendritic spine morphogenesis / regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of modification of postsynaptic actin cytoskeleton / cell-cell contact zone ...positive regulation of Schwann cell chemotaxis / regulation of non-canonical Wnt signaling pathway / regulation of dopaminergic neuron differentiation / extrinsic component of postsynaptic density membrane / Activated NTRK2 signals through CDK5 / regulation of epithelial to mesenchymal transition / positive regulation of dendritic spine morphogenesis / regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of modification of postsynaptic actin cytoskeleton / cell-cell contact zone / protein localization to membrane / cardiac muscle hypertrophy / activation of GTPase activity / Wnt signaling pathway, planar cell polarity pathway / regulation of small GTPase mediated signal transduction / main axon / neuron projection extension / small GTPase-mediated signal transduction / positive regulation of axonogenesis / NRAGE signals death through JNK / Rac protein signal transduction / CDC42 GTPase cycle / EPH-ephrin mediated repulsion of cells / RHOA GTPase cycle / positive regulation of epithelial to mesenchymal transition / RAC3 GTPase cycle / RAC2 GTPase cycle / ephrin receptor signaling pathway / axonal growth cone / RAC1 GTPase cycle / EPHB-mediated forward signaling / guanyl-nucleotide exchange factor activity / cell-matrix adhesion / regulation of ERK1 and ERK2 cascade / response to cocaine / receptor tyrosine kinase binding / ruffle membrane / kinase binding / G alpha (12/13) signalling events / cell-cell junction / cell migration / positive regulation of protein binding / microtubule binding / protein-containing complex assembly / microtubule / dendritic spine / positive regulation of cell migration / neuronal cell body / glutamatergic synapse / lipid binding / synapse / positive regulation of cell population proliferation / plasma membrane / cytosol
Similarity search - Function
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 domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Dbl homology (DH) domain superfamily ...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 domain / 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. / PDZ domain / Pdz3 Domain / 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. / PDZ domain / PDZ superfamily / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Rho guanine nucleotide exchange factor TIAM1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsShepherd, T.R. / Fuentes, E.J.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: The Tiam1 PDZ domain couples to Syndecan1 and promotes cell-matrix adhesion.
Authors: Shepherd, T.R. / Klaus, S.M. / Liu, X. / Ramaswamy, S. / DeMali, K.A. / Fuentes, E.J.
History
DepositionDec 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T-lymphoma invasion and metastasis-inducing protein 1


Theoretical massNumber of molelcules
Total (without water)10,1541
Polymers10,1541
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.782, 44.782, 70.799
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein T-lymphoma invasion and metastasis-inducing protein 1 / TIAM-1


Mass: 10154.440 Da / Num. of mol.: 1 / Fragment: PDZ Domain / Mutation: Q844H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TIAM1 / Plasmid: pET21a-6His-rTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13009
#2: 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: 2.02 Å3/Da / Density % sol: 39.05 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% (w/v) PEG 3350, 0.2 M NaSCN, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 16, 2007
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.3→34.025 Å / Num. all: 20526 / Num. obs: 20526 / % possible obs: 98.5 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 10.25 % / Biso Wilson estimate: 15.079 Å2 / Rmerge(I) obs: 0.05 / Χ2: 0.98 / Net I/σ(I): 18.5 / Scaling rejects: 1592
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 10 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 5.4 / Num. measured all: 19857 / Num. unique all: 1978 / Χ2: 1.33 / % possible all: 96.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å34.01 Å
Translation2.5 Å34.01 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.9Ldata scaling
PHASER1.3.3phasing
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
d*TREKdata reduction
MOLREPphasing
ARPmodel building
WARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→34.01 Å / Occupancy max: 1 / Occupancy min: 0.29 / SU ML: 0.21 / σ(F): 0.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.224 2009 9.8 %RANDOM
Rwork0.196 ---
obs0.199 20510 98.29 %-
all-20526 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.747 Å2 / ksol: 0.447 e/Å3
Displacement parametersBiso max: 36.16 Å2 / Biso mean: 16.266 Å2 / Biso min: 9.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.969 Å2-0 Å2-0 Å2
2--0.969 Å20 Å2
3----2.845 Å2
Refinement stepCycle: LAST / Resolution: 1.3→34.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms642 0 0 75 717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005696
X-RAY DIFFRACTIONf_angle_d0.995952
X-RAY DIFFRACTIONf_chiral_restr0.065114
X-RAY DIFFRACTIONf_plane_restr0.004122
X-RAY DIFFRACTIONf_dihedral_angle_d14.597266
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.3-1.3310.2221340.17112731407140796
1.331-1.3670.2181410.16312921433143397
1.367-1.4070.2191420.15612881430143098
1.407-1.4530.2011350.15712721407140798
1.453-1.5050.191450.15213211466146698
1.505-1.5650.2041430.15513041447144799
1.565-1.6360.1981350.15612941429142998
1.636-1.7220.2081510.17313451496149699
1.722-1.8310.2241390.17212991438143899
1.831-1.9720.2291460.1713431489148999
1.972-2.170.1691460.171133814841484100
2.17-2.4840.2281510.188136015111511100
2.484-3.1290.2581490.20713631512151299
3.129-34.0250.21520.20314091561156697

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