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- PDB-1xbr: T DOMAIN FROM XENOPUS LAEVIS BOUND TO DNA -

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Basic information

Entry
Database: PDB / ID: 1xbr
TitleT DOMAIN FROM XENOPUS LAEVIS BOUND TO DNA
Components
  • DNA (5'-D(*AP*AP*TP*TP*TP*CP*AP*CP*AP*CP*CP*TP*AP*GP*GP*TP*G P*TP*GP*AP*AP*AP* TP*T)-3')
  • PROTEIN (T PROTEIN)
KeywordsTRANSCRIPTION/DNA / COMPLEX (TRANSCRIPTION FACTOR-DNA) / TRANSCRIPTION FACTOR / DNA-BINDING PROTEIN / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


embryonic axis specification / determination of left/right symmetry / cell fate specification / mesoderm formation / somitogenesis / heart morphogenesis / cellular response to fibroblast growth factor stimulus / 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 ...embryonic axis specification / determination of left/right symmetry / cell fate specification / mesoderm formation / somitogenesis / heart morphogenesis / cellular response to fibroblast growth factor stimulus / 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 / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Transcription factor, T-box / 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 ...Transcription factor, T-box / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / T-box transcription factor T
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å
AuthorsMuller, C.W.
CitationJournal: Nature / Year: 1997
Title: Crystallographic structure of the T domain-DNA complex of the Brachyury transcription factor.
Authors: Muller, C.W. / Herrmann, B.G.
History
DepositionJul 16, 1997Deposition site: BNL / Processing site: NDB
Revision 1.0Jan 16, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*AP*AP*TP*TP*TP*CP*AP*CP*AP*CP*CP*TP*AP*GP*GP*TP*G P*TP*GP*AP*AP*AP* TP*T)-3')
D: DNA (5'-D(*AP*AP*TP*TP*TP*CP*AP*CP*AP*CP*CP*TP*AP*GP*GP*TP*G P*TP*GP*AP*AP*AP* TP*T)-3')
A: PROTEIN (T PROTEIN)
B: PROTEIN (T PROTEIN)


Theoretical massNumber of molelcules
Total (without water)56,8844
Polymers56,8844
Non-polymers00
Water2,576143
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.900, 113.900, 149.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (-0.999762, 0.020839, 0.006386), (0.02061, 0.999211, -0.033957), (-0.007089, -0.033818, -0.999403)
Vector: 36.1487, 3.8952, 233.1942)

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Components

#1: DNA chain DNA (5'-D(*AP*AP*TP*TP*TP*CP*AP*CP*AP*CP*CP*TP*AP*GP*GP*TP*G P*TP*GP*AP*AP*AP* TP*T)-3')


Mass: 7367.791 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Description: PALINDROMIC BINDING SITE OF THE T DOMAIN FROM AN IN VITRO SELECTION EXPERIMENT
#2: Protein PROTEIN (T PROTEIN)


Mass: 21074.268 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Tissue: EMBRYO
Description: EUKARYOTIC TRANSCRIPTION FACTOR, TRANSIENTLY EXPRESSED IN THE EMBRYO, REQUIRED FOR MESODERM FORMATION
Gene: XBRA / Plasmid: PT7-7 (NOVAGEN) / Species (production host): Escherichia coli / Cellular location (production host): CYTOSOL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P24781
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.45 Å3/Da / Density % sol: 52 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.2
Details: PROTEIN WAS CRYSTALLIZED FROM 2-8% PEG 8K, 20 MM MGCL2 50 MM NA-ACETATE, PH 4.2 1MM DTT, 5 MM SPERMINE, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2NACL11
3HEPES11
4DTT11
5WATER12
6PEG 800012
7MGCL212
8NA ACETATE12
9DTT12
10SPERMINE12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1996 / Details: MIRRORS
RadiationMonochromator: SI 111 CHANNEL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 22983 / % possible obs: 98.9 % / Redundancy: 4.4 % / Rsym value: 0.036 / Net I/σ(I): 33.5
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 13.7 / Rsym value: 0.136 / % possible all: 98.9
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 20 Å / % possible obs: 98.9 % / Redundancy: 4.4 % / Num. measured all: 101653
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.59 Å / % possible obs: 98.9 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.136 / Mean I/σ(I) obs: 13.7

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Processing

Software
NameVersionClassification
CCP4PROGRAMSmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 2.5→20 Å / Rfactor Rfree error: 0.02 / Data cutoff high absF: 1000000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.283 2262 9.8 %RANDOM
Rwork0.215 ---
obs0.215 22899 98.9 %-
Displacement parametersBiso mean: 26 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2954 978 0 143 4075
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.41
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.46
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.411.5
X-RAY DIFFRACTIONx_mcangle_it2.612
X-RAY DIFFRACTIONx_scbond_it2.822
X-RAY DIFFRACTIONx_scangle_it3.062.5
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Rms dev Biso : 1.85 Å2 / Rms dev position: 0.32 Å / Weight Biso : 1 / Weight position: 10

Ens-IDDom-IDNCS model details
11RESTRAINTS
22
LS refinement shellResolution: 2.5→2.61 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.359 279 9.6 %
Rwork0.306 2495 -
obs--98.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2DNA-RNA.PARAMTOPH19.PEP
X-RAY DIFFRACTION3PARAM19.SOLDNA-RNA.TOP
X-RAY DIFFRACTION4TOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 20 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.46
LS refinement shell
*PLUS
Rfactor obs: 0.306

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