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- PDB-3l46: Crystal structure of the second BRCT domain of epithelial cell tr... -

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Basic information

Entry
Database: PDB / ID: 3l46
TitleCrystal structure of the second BRCT domain of epithelial cell transforming 2 (ECT2)
ComponentsProtein ECT2
KeywordsSIGNALING PROTEIN / Guanine-nucleotide releasing factor / Phosphoprotein / Proto-oncogene / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


regulation of cytokinesis, actomyosin contractile ring assembly / centralspindlin complex / positive regulation of mitotic cytokinetic process / regulation of protein kinase activity / regulation of attachment of spindle microtubules to kinetochore / bicellular tight junction assembly / activation of GTPase activity / regulation of small GTPase mediated signal transduction / NRAGE signals death through JNK / RHOB GTPase cycle ...regulation of cytokinesis, actomyosin contractile ring assembly / centralspindlin complex / positive regulation of mitotic cytokinetic process / regulation of protein kinase activity / regulation of attachment of spindle microtubules to kinetochore / bicellular tight junction assembly / activation of GTPase activity / regulation of small GTPase mediated signal transduction / NRAGE signals death through JNK / RHOB GTPase cycle / activation of protein kinase activity / positive regulation of cytokinesis / cleavage furrow / mitotic cytokinesis / CDC42 GTPase cycle / RHOA GTPase cycle / bicellular tight junction / positive regulation of neuron differentiation / RAC1 GTPase cycle / cellular response to calcium ion / GTPase activator activity / positive regulation of GTPase activity / guanyl-nucleotide exchange factor activity / cellular response to ionizing radiation / cell morphogenesis / protein homooligomerization / mitotic spindle / small GTPase binding / cellular response to hydrogen peroxide / positive regulation of protein import into nucleus / cell-cell junction / G alpha (12/13) signalling events / 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
Guanine nucleotide exchange factor Ect2 / : / : / ECT2, PH domain / ECT2, BRCT0 domain / twin BRCT domain / BRCT domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Dbl homology (DH) domain superfamily ...Guanine nucleotide exchange factor Ect2 / : / : / ECT2, PH domain / ECT2, BRCT0 domain / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.482 Å
AuthorsNedyalkova, L. / Tempel, W. / Tong, Y. / Crombet, L. / Wang, H. / Guan, X. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. ...Nedyalkova, L. / Tempel, W. / Tong, Y. / Crombet, L. / Wang, H. / Guan, X. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of the second BRCT domain of epithelial cell transforming 2 (ECT2)
Authors: Nedyalkova, L. / Tempel, W. / Tong, Y. / Crombet, L. / Wang, H. / Guan, X. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionDec 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 17, 2014Group: Data collection / Version format compliance
Revision 1.3Oct 26, 2016Group: Other
Revision 1.4Nov 1, 2017Group: Refinement description / Category: software
Revision 1.5Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Protein ECT2
B: Protein ECT2


Theoretical massNumber of molelcules
Total (without water)26,2785
Polymers26,2782
Non-polymers03
Water2,144119
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-8 kcal/mol
Surface area9680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.158, 60.630, 74.004
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsAuthors state that the biological unit of this fragment is not known.

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Components

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


Mass: 13138.763 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ECT2 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q9H8V3
#2: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 3 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 1.8 Å3/Da / Density % sol: 31.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5M sodium citrate, 0.1M TRIS, 1:100 (w/w) subtilisin, pH 7.5, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.48→30 Å / Num. obs: 32244 / % possible obs: 100 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.088 / Χ2: 1.504 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.48-1.518.40.92816001.6321100
1.51-1.538.50.77815501.527199.9
1.53-1.568.50.67415811.471100
1.56-1.598.60.58115971.4741100
1.59-1.638.60.4916001.3831100
1.63-1.678.60.43715791.3341100
1.67-1.718.60.3715861.3521100
1.71-1.758.60.31416011.3281100
1.75-1.818.60.25915911.281100
1.81-1.868.60.215901.2871100
1.86-1.938.60.16216051.3621100
1.93-2.018.60.12616021.3991100
2.01-2.18.60.1116011.5241100
2.1-2.218.60.09716101.7051100
2.21-2.358.50.08716121.7921100
2.35-2.538.50.07416271.6741100
2.53-2.788.40.06116331.5791100
2.78-3.198.30.04716481.7231100
3.19-4.018.50.03516621.7141100
4.01-308.10.03217691.547199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2COU

2cou


Resolution: 1.482→25 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.192 / WRfactor Rwork: 0.173 / SU B: 1.098 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. ARP/WARP, COOT and the MOLPROBITY server were also used for refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1570 4.879 %thin shells (sftools)
Rwork0.181 ---
obs0.182 32180 99.929 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 10.175 Å2
Baniso -1Baniso -2Baniso -3
1--0.296 Å20 Å20 Å2
2---0.163 Å20 Å2
3---0.459 Å2
Refinement stepCycle: LAST / Resolution: 1.482→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1463 0 3 119 1585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221538
X-RAY DIFFRACTIONr_bond_other_d0.0010.021032
X-RAY DIFFRACTIONr_angle_refined_deg1.5511.9672096
X-RAY DIFFRACTIONr_angle_other_deg0.88532537
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0285197
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.90525.61673
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.01815261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.13154
X-RAY DIFFRACTIONr_chiral_restr0.0870.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211727
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02301
X-RAY DIFFRACTIONr_mcbond_it0.9411.5941
X-RAY DIFFRACTIONr_mcbond_other0.261.5378
X-RAY DIFFRACTIONr_mcangle_it1.66521526
X-RAY DIFFRACTIONr_scbond_it2.6043597
X-RAY DIFFRACTIONr_scangle_it4.1484.5563
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.482-1.520.2931360.2342169232499.182
1.52-1.5620.2081160.2122159227699.956
1.562-1.6070.2451010.21321252226100
1.607-1.6560.2231060.1882022212999.953
1.656-1.710.1781070.17420002107100
1.71-1.770.2021150.1791921203799.951
1.77-1.8360.2281040.17518651969100
1.836-1.9110.1881120.17317541866100
1.911-1.9950.1891150.17117131828100
1.995-2.0920.242360.17417121748100
2.092-2.2040.205920.17115581650100
2.204-2.3370.222560.17115331589100
2.337-2.4960.203540.17814251479100
2.496-2.6940.233750.18413081383100
2.694-2.9480.237550.2112331288100
2.948-3.290.239520.18511311183100
3.29-3.7880.16520.1669871039100
3.788-4.6130.131290.144877906100
4.613-6.4160.156310.189688719100
6.416-250.247260.19943045799.781

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