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- PDB-1tul: STRUCTURE OF TLP20 -

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Basic information

Entry
Database: PDB / ID: 1tul
TitleSTRUCTURE OF TLP20
ComponentsTLP20
KeywordsTELOKIN-LIKE PROTEIN
Function / homologyBaculovirus telokin-like protein 20 / Telokin-like protein, Tlp20, baculovirus / Baculovirus telokin-like protein 20 superfamily / Nucleopolyhedrovirus telokin-like protein-20 (TLP20) / Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A / Distorted Sandwich / Mainly Beta / Telokin-like protein 20
Function and homology information
Biological speciesAutographa californica nucleopolyhedrovirus
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsRayment, I. / Holden, H.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Molecular structure of a proteolytic fragment of TLP20.
Authors: Holden, H.M. / Wesenberg, G. / Raynes, D.A. / Hartshorne, D.J. / Guerriero, V. / Rayment, I.
History
DepositionAug 17, 1996Processing site: BNL
Revision 1.0Feb 17, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TLP20


Theoretical massNumber of molelcules
Total (without water)12,1801
Polymers12,1801
Non-polymers00
Water72140
1
A: TLP20

A: TLP20

A: TLP20


Theoretical massNumber of molelcules
Total (without water)36,5403
Polymers36,5403
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_564-z+1/2,-x+1,y-1/21
crystal symmetry operation10_655-y+1,z+1/2,-x+1/21
Buried area3760 Å2
ΔGint-32 kcal/mol
Surface area14400 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)76.300, 76.300, 76.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein TLP20


Mass: 12179.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Autographa californica nucleopolyhedrovirus
Genus: Nucleopolyhedrovirus / References: UniProt: Q06691
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.52 %
Crystal
*PLUS
Density % sol: 60 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop / Details: macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.8-0.9 Mammonium sulfate1drop
20.25 mM1dropNaN3
41.8 Mammonium sulfate1reservoir
3Na+/K+ succinate1drop

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Date: Sep 1, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 36733 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.048
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 50 Å / Num. obs: 7732 / Num. measured all: 36733
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / Num. unique obs: 927 / Num. measured obs: 2394 / Rmerge(I) obs: 0.242

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Processing

Software
NameClassification
TNTrefinement
XDSdata reduction
RefinementResolution: 2.2→30 Å / σ(F): 0
Details: TNT MEAN B (A**2) :24.9 (BACKBONE) PLANAR 1-4 DISTANCE :.004
RfactorNum. reflection% reflection
Rwork0.181 --
obs-7727 99.8 %
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms811 0 0 40 851
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.014
X-RAY DIFFRACTIONt_angle_deg1.93
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_deg18.7
X-RAY DIFFRACTIONt_plane_restr0.013

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