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- PDB-3djn: Crystal structure of mouse TIS21 -

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Basic information

Entry
Database: PDB / ID: 3djn
TitleCrystal structure of mouse TIS21
ComponentsProtein BTG2
KeywordsTRANSCRIPTION / beta-alpha-barrels / Transcription regulation
Function / homology
Function and homology information


TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / negative regulation of neural precursor cell proliferation / protein methylation / dentate gyrus development / anterior/posterior pattern specification / central nervous system neuron development / skeletal muscle cell differentiation / associative learning / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of mitotic cell cycle ...TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / negative regulation of neural precursor cell proliferation / protein methylation / dentate gyrus development / anterior/posterior pattern specification / central nervous system neuron development / skeletal muscle cell differentiation / associative learning / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of mitotic cell cycle / response to electrical stimulus / response to mechanical stimulus / neuron differentiation / response to organic cyclic compound / response to peptide hormone / DNA-binding transcription repressor activity, RNA polymerase II-specific / neuron projection development / negative regulation of neuron apoptotic process / negative regulation of translation / negative regulation of cell population proliferation / DNA damage response / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
Protein BTG2 / Anti-proliferative protein, N-terminal domain / BTG family signature 1. / BTG family signature 2. / Anti-proliferative protein / BTG-like domain superfamily / BTG family / tob/btg1 family / Actin; Chain A, domain 4 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsYang, X. / Morita, M. / Wang, H. / Suzuki, T. / Bartlam, M. / Yamamoto, T.
CitationJournal: Nucleic Acids Res. / Year: 2008
Title: Crystal structures of human BTG2 and mouse TIS21 involved in suppression of CAF1 deadenylase activity
Authors: Yang, X. / Morita, M. / Wang, H. / Suzuki, T. / Yang, W. / Luo, Y. / Zhao, C. / Yu, Y. / Bartlam, M. / Yamamoto, T. / Rao, Z.
History
DepositionJun 24, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Protein BTG2


Theoretical massNumber of molelcules
Total (without water)13,4581
Polymers13,4581
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.020, 39.704, 83.695
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein BTG2 / NGF-inducible protein TIS21


Mass: 13458.454 Da / Num. of mol.: 1 / Fragment: UNP residues 8-125
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tis21 / Plasmid: pGEX6p1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q04211
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.35 Å3/Da / Density % sol: 47.59 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM BIS-TRIS, 23% (v/v) PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 15, 2007 / Details: osmic mirror
RadiationMonochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 6923 / Num. obs: 6868 / Observed criterion σ(F): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.115

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2D5R

2d5r


Resolution: 2.2→34.62 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.9 / SU B: 14.004 / SU ML: 0.162 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.311 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26162 681 10 %RANDOM
Rwork0.1958 ---
all0.271 6868 --
obs0.20228 6149 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.584 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20 Å20 Å2
2--0.56 Å20 Å2
3----1.49 Å2
Refinement stepCycle: LAST / Resolution: 2.2→34.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms945 0 0 73 1018
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021965
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.9691304
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6255119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.45722.61942
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.79515168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.594158
X-RAY DIFFRACTIONr_chiral_restr0.0960.2141
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02723
X-RAY DIFFRACTIONr_nbd_refined0.220.2439
X-RAY DIFFRACTIONr_nbtor_refined0.3020.2648
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.257
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.260.28
X-RAY DIFFRACTIONr_mcbond_it0.6941.5608
X-RAY DIFFRACTIONr_mcangle_it1.1562954
X-RAY DIFFRACTIONr_scbond_it1.8113409
X-RAY DIFFRACTIONr_scangle_it2.8984.5349
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 43 -
Rwork0.21 438 -
obs-6868 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7805-0.27660.42571.3998-0.50792.2136-0.05310.0953-0.0190.01870.0039-0.05160.015-0.13380.0492-0.0674-0.0142-0.0055-0.0093-0.004-0.037115.9856.93811.5628
20.3502-0.2403-0.12490.5737-0.63261.30680.01820.0178-0.01820.10120.03180.0447-0.0379-0.0908-0.05-0.0331-0.0270.0077-0.0465-0.0152-0.003217.35216.195710.9362
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1BA8 - 1251 - 118
2X-RAY DIFFRACTION2BB126 - 1981 - 73

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