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- PDB-7hi8: PanDDA analysis group deposition -- Crystal Structure of ground s... -

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Basic information

Entry
Database: PDB / ID: 7hi8
TitlePanDDA analysis group deposition -- Crystal Structure of ground state model of human Brachyury
ComponentsT-box transcription factor T
KeywordsTRANSCRIPTION / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer
Function / homology
Function and homology information


primitive streak formation / anterior/posterior axis specification, embryo / Epithelial-Mesenchymal Transition (EMT) during gastrulation / cardiac muscle cell myoblast differentiation / Germ layer formation at gastrulation / Formation of definitive endoderm / Formation of axial mesoderm / cell fate specification / Cardiogenesis / Formation of paraxial mesoderm ...primitive streak formation / anterior/posterior axis specification, embryo / Epithelial-Mesenchymal Transition (EMT) during gastrulation / cardiac muscle cell myoblast differentiation / Germ layer formation at gastrulation / Formation of definitive endoderm / Formation of axial mesoderm / cell fate specification / Cardiogenesis / Formation of paraxial mesoderm / mesoderm development / mesoderm formation / somitogenesis / heart morphogenesis / sequence-specific double-stranded DNA binding / transcription corepressor activity / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
Transcription factor, Brachyury / T-box transcription factor / Transcription factor, T-box, conserved site / T-box superfamily / T-box transcription factor, DNA-binding domain / T-box domain signature 2. / T-box domain signature 1. / T-box domain profile. / Domain first found in the mice T locus (Brachyury) protein / T-box / p53-like transcription factor, DNA-binding
Similarity search - Domain/homology
: / T-box transcription factor T
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.54 Å
AuthorsNewman, J.A. / Gavard, A.E. / Sherestha, L. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: To Be Published
Title: PanDDA analysis group deposition
Authors: Newman, J.A. / Gavard, A.E. / Sherestha, L. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O.
History
DepositionSep 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T-box transcription factor T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2576
Polymers19,6951
Non-polymers5625
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)60.318, 60.318, 110.014
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein T-box transcription factor T / Brachyury protein / Protein T


Mass: 19694.701 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TBXT, T / Production host: Escherichia coli (E. coli) / References: UniProt: O15178
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.54 Å3/Da / Density % sol: 51.58 % / Mosaicity: 0 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 0.1 M CdCl, 0.1 M Acetate pH 4.5, 32% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.54→52.89 Å / Num. obs: 30834 / % possible obs: 99.98 % / Redundancy: 12.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.037 / Rrim(I) all: 0.132 / Net I/σ(I): 12.9 / Num. measured all: 171699 / Scaling rejects: 0
Reflection shellResolution: 1.54→1.59 Å / Redundancy: 10 % / Rmerge(I) obs: 2 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2746 / CC1/2: 0.645 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
Aimless0.7.1data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6f58

6f58


Resolution: 1.54→52.89 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.751 / SU ML: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.187 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2411 1536 4.98 %RANDOM
Rwork0.2268 ---
obs0.2275 30834 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.42 Å2
Refinement stepCycle: final / Resolution: 1.54→52.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1376 0 0 75 1451
Biso mean---37.94 -
Num. residues----172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811423
X-RAY DIFFRACTIONf_angle_d0.98111933
X-RAY DIFFRACTIONf_chiral_restr0.0577205
X-RAY DIFFRACTIONf_plane_restr0.0084250
X-RAY DIFFRACTIONf_dihedral_angle_d15.5251529
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.590.39041430.3492603X-RAY DIFFRACTION99.78
1.59-1.650.35291560.33872589X-RAY DIFFRACTION99.78
1.65-1.710.26211360.29392602X-RAY DIFFRACTION99.96
1.71-1.790.31351520.25972605X-RAY DIFFRACTION99.89
1.79-1.880.26181350.25282638X-RAY DIFFRACTION99.96
1.88-20.27421300.26632632X-RAY DIFFRACTION100
2-2.160.25811340.24232663X-RAY DIFFRACTION100
2.16-2.370.21611390.23562649X-RAY DIFFRACTION99.93
2.37-2.720.22431440.24032693X-RAY DIFFRACTION100
2.72-3.420.24511300.22792722X-RAY DIFFRACTION100
3.43-52.890.21431370.19152911X-RAY DIFFRACTION99.97

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