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- PDB-3eop: Crystal Structure of the DUF55 domain of human thymocyte nuclear ... -

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Basic information

Entry
Database: PDB / ID: 3eop
TitleCrystal Structure of the DUF55 domain of human thymocyte nuclear protein 1
ComponentsThymocyte nuclear protein 1
KeywordsUNKNOWN FUNCTION / Nucleus / Phosphoprotein
Function / homology
Function and homology information


: / : / EVE domain / EVE domain / ph1033 like fold / ph1033 like domains / PUA-like superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Thymocyte nuclear protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsYu, F. / Song, A. / Xu, C. / Sun, L. / Li, L. / Tang, L. / Hu, H. / He, J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Determining the DUF55-domain structure of human thymocyte nuclear protein 1 from crystals partially twinned by tetartohedry
Authors: Yu, F. / Song, A. / Xu, C. / Sun, L. / Li, J. / Tang, L. / Yu, M. / Yeates, T.O. / Hu, H. / He, J.
History
DepositionSep 29, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thymocyte nuclear protein 1
B: Thymocyte nuclear protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9266
Polymers41,5412
Non-polymers3844
Water66737
1
A: Thymocyte nuclear protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9633
Polymers20,7711
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thymocyte nuclear protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9633
Polymers20,7711
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.258, 51.258, 122.400
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Thymocyte nuclear protein 1 / Thymocyte protein Thy28


Mass: 20770.738 Da / Num. of mol.: 2 / Fragment: DUF55 domain, UNP residues 55-221
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET22 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) pLysS / References: UniProt: Q9P016
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 10.9
Details: 0.1M NaAc (pH 4.0-4.8), 28% PEG 2000 MME, 200mM (NH4)2SO4, 3% 1,6-diaminohexane as additive, pH 10.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→44.41 Å / Num. all: 15997 / Num. obs: 15931 / % possible obs: 99.4 % / Redundancy: 4.8 % / Biso Wilson estimate: 40.06 Å2 / Rmerge(I) obs: 0.056
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.291 / Num. unique all: 2326 / % possible all: 98.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2ar1

2ar1


Resolution: 2.3→44.39 Å / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 0 / σ(F): 0
Details: Thin resolution shells. Quadruplets of twin related reflections were kept together in either the test set or the refinement set throughout refinement.
RfactorNum. reflection% reflection
Rfree0.2378 1422 8.2 %
Rwork0.1823 --
obs-15463 96.7 %
Solvent computationBsol: 59.208 Å2
Displacement parametersBiso max: 68.11 Å2 / Biso mean: 36.2394 Å2 / Biso min: 5.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.031 Å2-0.085 Å2-0 Å2
2--0.031 Å2-0 Å2
3----0.062 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.3→44.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2719 0 20 37 2776
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.4071.5
X-RAY DIFFRACTIONc_scbond_it1.7562
X-RAY DIFFRACTIONc_mcangle_it2.2962
X-RAY DIFFRACTIONc_scangle_it2.4452.5
X-RAY DIFFRACTIONc_bond_d0.00602
X-RAY DIFFRACTIONc_angle_d1.17062
X-RAY DIFFRACTIONc_dihedral_angle_d22.63209
X-RAY DIFFRACTIONo_improper_angle_d0.79878
LS refinement shellResolution: 2.3→2.38 Å
RfactorNum. reflection% reflection
Rfree0.3186 119 -
Rwork0.2513 --
obs-1255 91.36 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param

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