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- PDB-4n40: Crystal structure of human Epithelial cell-transforming sequence ... -

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Basic information

Entry
Database: PDB / ID: 4n40
TitleCrystal structure of human Epithelial cell-transforming sequence 2 protein
ComponentsProtein ECT2
KeywordsCELL CYCLE / triple brct domains
Function / homology
Function and homology information


regulation of cytokinesis, actomyosin contractile ring assembly / centralspindlin complex / regulation of attachment of spindle microtubules to kinetochore / bicellular tight junction assembly / activation of GTPase activity / regulation of protein kinase activity / regulation of small GTPase mediated signal transduction / RHOB GTPase cycle / NRAGE signals death through JNK / positive regulation of cytokinesis ...regulation of cytokinesis, actomyosin contractile ring assembly / centralspindlin complex / regulation of attachment of spindle microtubules to kinetochore / bicellular tight junction assembly / activation of GTPase activity / regulation of protein kinase activity / regulation of small GTPase mediated signal transduction / RHOB GTPase cycle / NRAGE signals death through JNK / positive regulation of cytokinesis / activation of protein kinase activity / cleavage furrow / CDC42 GTPase cycle / mitotic cytokinesis / bicellular tight junction / RHOA GTPase cycle / RAC1 GTPase cycle / cellular response to calcium ion / positive regulation of neuron differentiation / GTPase activator activity / guanyl-nucleotide exchange factor activity / cellular response to ionizing radiation / protein homooligomerization / cell morphogenesis / mitotic spindle / cellular response to hydrogen peroxide / small GTPase binding / positive regulation of GTPase activity / positive regulation of protein import into nucleus / G alpha (12/13) signalling events / cell-cell junction / protein transport / nervous system development / cell cortex / midbody / positive regulation of canonical NF-kappaB signal transduction / cell differentiation / nuclear body / intracellular signal transduction / positive regulation of apoptotic process / centrosome / protein homodimerization activity / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
: / : / ECT2, PH domain / ECT2, BRCT0 domain / Guanine nucleotide exchange factor Ect2 / twin BRCT domain / BRCT domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Dbl homology (DH) domain superfamily ...: / : / ECT2, PH domain / ECT2, BRCT0 domain / Guanine nucleotide exchange factor Ect2 / twin BRCT domain / BRCT domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / 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. / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / PH-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.106 Å
AuthorsZou, Y. / Shao, Z.H. / Li, F.D. / Gong, D. / Wang, C. / Gong, Q. / Shi, Y.
CitationJournal: Febs Lett. / Year: 2014
Title: Crystal structure of triple-BRCT-domain of ECT2 and insights into the binding characteristics to CYK-4
Authors: Zou, Y. / Shao, Z.H. / Peng, J. / Li, F.D. / Gong, D. / Wang, C. / Zuo, X. / Zhang, Z. / Wu, J. / Shi, Y. / Gong, Q.
History
DepositionOct 8, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein ECT2


Theoretical massNumber of molelcules
Total (without water)33,0731
Polymers33,0731
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Protein ECT2

A: Protein ECT2

A: Protein ECT2


Theoretical massNumber of molelcules
Total (without water)99,2203
Polymers99,2203
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area3050 Å2
ΔGint-22 kcal/mol
Surface area42540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.700, 123.700, 89.244
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Protein ECT2 / Epithelial cell-transforming sequence 2 oncogene


Mass: 33073.285 Da / Num. of mol.: 1 / Fragment: UNP residues, Isoform 4, 45-325
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ECT2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9H8V3
Sequence detailsTHE REFERENCE SEQUENCE OF THIS PROTEIN IS ISOFORM 4 OF Q9H8V3.

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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: 4.01 Å3/Da / Density % sol: 69.35 % / Mosaicity: 0.396 °
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100mM MES, 14% MPEG 5000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRF BL17U10.9793
SYNCHROTRONSSRF BL17U20.9793
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDApr 20, 2012
ADSC QUANTUM 315r2CCDMay 6, 2012
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1plane gratingSINGLE WAVELENGTHMx-ray1
2plane gratingSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 9170 / Num. obs: 9161 / % possible obs: 99.9 % / Redundancy: 4.4 % / Biso Wilson estimate: 106.42 Å2 / Rmerge(I) obs: 0.098 / Χ2: 0.947 / Net I/σ(I): 8.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.1-3.154.40.9564340.6781,299.8
3.15-3.214.40.7444650.8341,2100
3.21-3.274.40.5784420.7181,2100
3.27-3.344.40.5474820.7021,2100
3.34-3.414.40.3954530.691,2100
3.41-3.494.40.3244630.7671,2100
3.49-3.584.40.2664580.8291,2100
3.58-3.684.40.2154700.8821,2100
3.68-3.784.40.1794351.0241,2100
3.78-3.914.40.1614771.0791,2100
3.91-4.044.40.1374651.0471,2100
4.04-4.214.40.1164571.0361,2100
4.21-4.44.40.1084551.0981,2100
4.4-4.634.40.094641.0671,2100
4.63-4.924.30.0744491.0991,299.8
4.92-5.34.30.0734620.9741,2100
5.3-5.834.20.0864681.161,299.8
5.83-6.674.50.0774440.9491,2100
6.67-8.44.50.0774671.2461,2100
8.4-504.30.0724511.0751,297.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
PHENIX1.6.1_357refinement
RefinementMethod to determine structure: SAD / Resolution: 3.106→36.873 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7386 / SU ML: 0.48 / σ(F): 1.98 / Phase error: 32.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2814 437 4.77 %RANDOM
Rwork0.2138 ---
obs0.2169 9156 99.85 %-
all-9170 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.927 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso max: 194.18 Å2 / Biso mean: 112.1665 Å2 / Biso min: 71.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.3177 Å20 Å20 Å2
2---0.3177 Å2-0 Å2
3---0.6353 Å2
Refinement stepCycle: LAST / Resolution: 3.106→36.873 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2142 0 0 0 2142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122198
X-RAY DIFFRACTIONf_angle_d1.6552988
X-RAY DIFFRACTIONf_chiral_restr0.101337
X-RAY DIFFRACTIONf_plane_restr0.007386
X-RAY DIFFRACTIONf_dihedral_angle_d15.811782
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.1063-3.55550.39011510.31229113062
3.5555-4.47830.2621450.211628993044
4.4783-36.87530.26341410.191329093050

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