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- PDB-4in0: Crystal Structure of human splicing factor dim2/TXNL4B -

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Basic information

Entry
Database: PDB / ID: 4in0
TitleCrystal Structure of human splicing factor dim2/TXNL4B
ComponentsThioredoxin-like protein 4B
KeywordsSPLICING / pre-mRNA splicing
Function / homology
Function and homology information


U5 snRNP / U4/U6 x U5 tri-snRNP complex / spliceosomal complex / mRNA splicing, via spliceosome / nucleoplasm / cytosol
Similarity search - Function
Dim1 family / Mitosis protein DIM1 / Mitosis protein DIM1 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
sucrose / Thioredoxin-like protein 4B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.327 Å
AuthorsJin, T.C. / Guo, F. / Zhang, Y.Z.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: High-resolution crystal structure of human Dim2/TXNL4B.
Authors: Jin, T. / Guo, F. / Wang, Y. / Zhang, Y.
History
DepositionJan 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _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
A: Thioredoxin-like protein 4B
B: Thioredoxin-like protein 4B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1493
Polymers33,8072
Non-polymers3421
Water6,882382
1
A: Thioredoxin-like protein 4B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2462
Polymers16,9031
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thioredoxin-like protein 4B


Theoretical massNumber of molelcules
Total (without water)16,9031
Polymers16,9031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.325, 63.640, 51.148
Angle α, β, γ (deg.)90.000, 92.290, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Thioredoxin-like protein 4B / dim2 / TXNL4B / Dim1-like protein


Mass: 16903.416 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DIM2, DLP, TXNL4B / Plasmid: pET29 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9NX01
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 1.89 Å3/Da / Density % sol: 34.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% PEG8000, 0.2 M magnesium acetate tetrahydate, 0.1 M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 5, 2005
RadiationMonochromator: Rosenbaum-Rock double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.327→30.567 Å / Num. all: 58146 / Num. obs: 56401 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XBS

1xbs


Resolution: 1.327→30.567 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.1928 / WRfactor Rwork: 0.1309 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8751 / SU B: 1.946 / SU ML: 0.036 / SU R Cruickshank DPI: 0.057 / SU Rfree: 0.0591 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1849 2164 4 %RANDOM
Rwork0.1279 ---
obs0.1303 54157 92.96 %-
all-56401 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 137.58 Å2 / Biso mean: 23.1496 Å2 / Biso min: 6.96 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å20.24 Å2
2--1.32 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.327→30.567 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2239 0 23 382 2644
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.022491
X-RAY DIFFRACTIONr_bond_other_d0.0010.022446
X-RAY DIFFRACTIONr_angle_refined_deg2.1891.9923407
X-RAY DIFFRACTIONr_angle_other_deg1.07935716
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9795333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00525.234107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.17915482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg30.328159
X-RAY DIFFRACTIONr_chiral_restr0.1410.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212777
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02528
X-RAY DIFFRACTIONr_mcbond_it3.0041.7521191
X-RAY DIFFRACTIONr_mcbond_other2.9791.7491190
X-RAY DIFFRACTIONr_mcangle_it3.3962.6521501
X-RAY DIFFRACTIONr_rigid_bond_restr5.89634937
X-RAY DIFFRACTIONr_sphericity_free59.449587
X-RAY DIFFRACTIONr_sphericity_bonded18.23755158
LS refinement shellResolution: 1.327→1.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 129 -
Rwork0.157 3130 -
all-3259 -
obs--75.44 %

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