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- PDB-7hi9: PanDDA analysis group deposition of ground-state model of human B... -

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Basic information

Entry
Database: PDB / ID: 7hi9
TitlePanDDA analysis group deposition of ground-state model of human Brachyury G177D variant
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: 1.42 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 of ground-state model
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)19,7762
Polymers19,7531
Non-polymers231
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.734, 99.734, 99.325
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-485-

HOH

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Components

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


Mass: 19752.738 Da / Num. of mol.: 1 / Mutation: G177D
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.41 Å3/Da / Density % sol: 48.89 % / Mosaicity: 0 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M SPG pH 7.0, 30 % PEG 1000

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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: Dec 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.42→49.86 Å / Num. obs: 35889 / % possible obs: 100 % / Redundancy: 8.2 % / CC1/2: 1 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.013 / Rrim(I) all: 0.04 / Net I/σ(I): 21 / Num. measured all: 295722 / Scaling rejects: 238
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.42-1.465.21.1981358526070.5620.5751.3321.2100
6.35-49.868.90.022398645010.0080.0247399.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6f58

6f58


Resolution: 1.42→49.87 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.501 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2231 1709 4.8 %RANDOM
Rwork0.1975 ---
obs0.1988 34177 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 max: 92.2 Å2 / Biso mean: 23.583 Å2 / Biso min: 13.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å2-0.23 Å2-0 Å2
2---0.46 Å2-0 Å2
3---1.51 Å2
Refinement stepCycle: final / Resolution: 1.42→49.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1380 0 1 187 1568
Biso mean--90.9 35.52 -
Num. residues----171
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131466
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171356
X-RAY DIFFRACTIONr_angle_refined_deg1.7151.6451992
X-RAY DIFFRACTIONr_angle_other_deg1.4281.5723160
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0345179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.4422.43274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69815255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.633158
X-RAY DIFFRACTIONr_chiral_restr0.0880.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021637
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02307
X-RAY DIFFRACTIONr_mcbond_it1.9362.224710
X-RAY DIFFRACTIONr_mcbond_other1.9192.221709
X-RAY DIFFRACTIONr_mcangle_it2.9893.325890
LS refinement shellResolution: 1.42→1.457 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 124 -
Rwork0.321 2483 -
all-2607 -
obs--99.58 %

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