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- PDB-1nq3: Crystal structure of the mammalian tumor associated antigen UK114 -

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Basic information

Entry
Database: PDB / ID: 1nq3
TitleCrystal structure of the mammalian tumor associated antigen UK114
Components14.3 kDa perchloric acid soluble protein
KeywordsImmune system / metal binding protein / tumor associated antigen / YER057c/YIL051c/YjgF protein family / UK114 / trimer
Function / homology
Function and homology information


: / 2-iminobutanoate/2-iminopropanoate deaminase / 2-iminobutanoate deaminase activity / 2-iminopropanoate deaminase activity / mRNA destabilization / mRNA catabolic process / lipid metabolic process / RNA endonuclease activity, producing 3'-phosphomonoesters / peroxisome / Hydrolases; Acting on ester bonds ...: / 2-iminobutanoate/2-iminopropanoate deaminase / 2-iminobutanoate deaminase activity / 2-iminopropanoate deaminase activity / mRNA destabilization / mRNA catabolic process / lipid metabolic process / RNA endonuclease activity, producing 3'-phosphomonoesters / peroxisome / Hydrolases; Acting on ester bonds / negative regulation of translation / mitochondrial matrix / mRNA binding / nucleus / cytosol
Similarity search - Function
RidA, conserved site / Uncharacterized protein family UPF0076 signature. / RidA family / RutC-like / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like superfamily / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2-iminobutanoate/2-iminopropanoate deaminase
Similarity search - Component
Biological speciesCapra hircus (goat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDeriu, D. / Briand, C. / Mistiniene, E. / Naktinis, V. / Grutter, M.G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structure and oligomeric state of the mammalian tumour-associated antigen UK114.
Authors: Deriu, D. / Briand, C. / Mistiniene, E. / Naktinis, V. / Grutter, M.G.
History
DepositionJan 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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

Downloads & links

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Assembly

Deposited unit
A: 14.3 kDa perchloric acid soluble protein
B: 14.3 kDa perchloric acid soluble protein
C: 14.3 kDa perchloric acid soluble protein
D: 14.3 kDa perchloric acid soluble protein
E: 14.3 kDa perchloric acid soluble protein
F: 14.3 kDa perchloric acid soluble protein


Theoretical massNumber of molelcules
Total (without water)85,0696
Polymers85,0696
Non-polymers00
Water4,666259
1
A: 14.3 kDa perchloric acid soluble protein
B: 14.3 kDa perchloric acid soluble protein
C: 14.3 kDa perchloric acid soluble protein


Theoretical massNumber of molelcules
Total (without water)42,5343
Polymers42,5343
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-33 kcal/mol
Surface area15180 Å2
MethodPISA
2
D: 14.3 kDa perchloric acid soluble protein
E: 14.3 kDa perchloric acid soluble protein
F: 14.3 kDa perchloric acid soluble protein


Theoretical massNumber of molelcules
Total (without water)42,5343
Polymers42,5343
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6900 Å2
ΔGint-33 kcal/mol
Surface area15260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.035, 77.998, 192.510
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
14.3 kDa perchloric acid soluble protein / UK114 TUMOR ASSOCIATED ANTIGEN


Mass: 14178.159 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Capra hircus (goat) / Plasmid: pT7a / Production host: Escherichia coli (E. coli) / Strain (production host): K802 / References: UniProt: P80601
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.23 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 8000, potassium phosphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 291 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
111 mg/mlprotein1drop
222 %(w/v)PEG80001reservoir
350 mMpotassium phosphate1reservoirpH5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.006 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 19, 2001
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.006 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 39643 / Num. obs: 39547 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 27.11 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 20.14
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.45 / Num. unique all: 3812 / % possible all: 96
Reflection
*PLUS
Lowest resolution: 20 Å
Reflection shell
*PLUS
% possible obs: 96 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QD9 (serine model)

1qd9


Resolution: 2.2→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2255 1981 5 %RANDOM
Rwork0.1875 ---
all-39643 --
obs-39547 --
Displacement parametersBiso mean: 27.11 Å2
Baniso -1Baniso -2Baniso -3
1--1.339 Å20 Å20 Å2
2--1.822 Å20 Å2
3----0.483 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.299 Å0.238 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2802 Å0.1933 Å
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5859 0 0 259 6118
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
2.2-2.220.29480.252X-RAY DIFFRACTION1011
2.22-2.240.29500.252X-RAY DIFFRACTION954
2.24-2.260.29470.252X-RAY DIFFRACTION993
2.26-2.280.29530.252X-RAY DIFFRACTION997
2.28-2.30.29480.252X-RAY DIFFRACTION1017
2.3-2.330.29540.252X-RAY DIFFRACTION1011
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.226 / Rfactor Rwork: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.2

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