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- PDB-4nxp: Crystal Structure of Free T-cell Lymphoma Invasion and Metastasis... -

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Basic information

Entry
Database: PDB / ID: 4nxp
TitleCrystal Structure of Free T-cell Lymphoma Invasion and Metastasis-1 PDZ Domain Quadruple Mutant (QM)
ComponentsT-lymphoma invasion and metastasis-inducing protein 1
KeywordsSIGNALING PROTEIN / Beta barrel fold protein / PDZ domain / peptide binding / specificity mutant / scaffold signaling protein for cell adhesion and cell junction / signaling domain
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 / regulation of modification of postsynaptic actin cytoskeleton / regulation of insulin secretion involved in cellular response to glucose stimulus / positive regulation of dendritic spine morphogenesis / 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 / regulation of modification of postsynaptic actin cytoskeleton / regulation of insulin secretion involved in cellular response to glucose stimulus / positive regulation of dendritic spine morphogenesis / cell-cell contact zone / protein localization to membrane / cardiac muscle hypertrophy / activation of GTPase activity / regulation of small GTPase mediated signal transduction / Wnt signaling pathway, planar cell polarity pathway / neuron projection extension / positive regulation of axonogenesis / small GTPase-mediated signal transduction / main axon / NRAGE signals death through JNK / Rac protein signal transduction / CDC42 GTPase cycle / EPH-ephrin mediated repulsion of cells / RHOA GTPase cycle / ephrin receptor signaling pathway / RAC2 GTPase cycle / RAC3 GTPase cycle / axonal growth cone / positive regulation of epithelial to mesenchymal transition / EPHB-mediated forward signaling / RAC1 GTPase cycle / regulation of ERK1 and ERK2 cascade / cell-matrix adhesion / guanyl-nucleotide exchange factor activity / response to cocaine / receptor tyrosine kinase binding / kinase binding / ruffle membrane / cell-cell junction / G alpha (12/13) signalling events / cell migration / positive regulation of protein binding / protein-containing complex assembly / microtubule binding / microtubule / dendritic spine / positive regulation of cell migration / neuronal cell body / lipid binding / glutamatergic synapse / positive regulation of cell population proliferation / synapse / plasma membrane / cytosol
Similarity search - Function
TIAM1, CC-Ex domain / Tiam1/Tiam2/Protein still life / T-lymphoma invasion and metastasis CC-Ex domain / Tiam1 second PH domain-like / 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 ...TIAM1, CC-Ex domain / Tiam1/Tiam2/Protein still life / T-lymphoma invasion and metastasis CC-Ex domain / Tiam1 second PH domain-like / 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. / PDZ domain / Pleckstrin homology domain. / Pleckstrin homology 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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLiu, X. / Speckhard, D.C. / Shepherd, T.R. / Hengel, S.R. / Fuentes, E.J.
CitationJournal: Structure / Year: 2016
Title: Distinct Roles for Conformational Dynamics in Protein-Ligand Interactions.
Authors: Liu, X. / Speckhard, D.C. / Shepherd, T.R. / Sun, Y.J. / Hengel, S.R. / Yu, L. / Fowler, C.A. / Gakhar, L. / Fuentes, E.J.
History
DepositionDec 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Database references
Revision 1.2Dec 21, 2022Group: 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 1.3Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)10,1921
Polymers10,1921
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.843, 45.843, 71.362
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-1025-

HOH

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Components

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


Mass: 10192.402 Da / Num. of mol.: 1 / Fragment: PDZ domain / Mutation: L911M, K912E, L915F, L920V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: 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


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.12 Å3/Da / Density % sol: 42.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 1.5M Ammonium Sulfate, 0.1M Tris, pH=8.5, 12% Glycerol, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 21, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.888
11-h,-k,l20.112
ReflectionResolution: 2.3→19.85 Å / Num. all: 4117 / Num. obs: 3866 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.18 % / Biso Wilson estimate: 34.3 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 7.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.17 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 2.1 / % possible all: 97.3

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.7.0032refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3KZD

3kzd


Resolution: 2.3→19.85 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.903 / SU B: 7.454 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25777 168 4.3 %RANDOM
Rwork0.21693 ---
obs0.21873 3697 93.4 %-
all-3958 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.409 Å2
Baniso -1Baniso -2Baniso -3
1-9.21 Å20 Å20 Å2
2--9.21 Å20 Å2
3----18.42 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms666 0 0 47 713
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.019674
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0981.982905
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.571584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.2324.66730
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.37615125
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.499154
X-RAY DIFFRACTIONr_chiral_restr0.0660.2103
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02497
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9982.999341
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7974.496424
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.1293.15331
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.80724.843964
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: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 21 -
Rwork0.297 265 -
obs-286 97.95 %

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