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- PDB-2ivo: Structure of UP1 protein -

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Basic information

Entry
Database: PDB / ID: 2ivo
TitleStructure of UP1 protein
ComponentsUP1
KeywordsHYDROLASE / UP1 KEOPS COMPLEX / FE/ZN DEPENDENT NUCLEOTIDE PHOSPHATASE / METALLOPROTEASE / HYPOTHETICAL PROTEIN / ZINC / PROTEASE / METAL-BINDING
Function / homology
Function and homology information


N6-L-threonylcarbamoyladenine synthase / N(6)-L-threonylcarbamoyladenine synthase activity / EKC/KEOPS complex / tRNA threonylcarbamoyladenosine modification / tRNA binding / single-stranded RNA binding / iron ion binding / cytoplasm
Similarity search - Function
tRNA N6-adenosine threonylcarbamoyltransferase Kae1, archaea and eukaryote / Peptidase M22, conserved site / Glycoprotease family signature. / Kae1/TsaD family / Gcp-like domain / tRNA N6-adenosine threonylcarbamoyltransferase / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
TUNGSTATE(VI)ION / tRNA N6-adenosine threonylcarbamoyltransferase
Similarity search - Component
Biological speciesPYROCOCCUS ABYSSI (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsHecker, A. / Leulliot, N. / Graille, M. / Dorlet, P. / Quevillon-Cheruel, S. / Ulryck, N. / Van Tilbeurgh, H. / Forterre, P.
CitationJournal: Nucleic Acids Res. / Year: 2007
Title: An Archaeal Orthologue of the Universal Protein Kae1 is an Iron Metalloprotein which Exhibits Atypical DNA-Binding Properties and Apurinic-Endonuclease Activity in Vitro.
Authors: Hecker, A. / Leulliot, N. / Gadelle, D. / Graille, M. / Justome, A. / Dorlet, P. / Brochier, C. / Quevillon-Cheruel, S. / Le Cam, E. / Van Tilbeurgh, H. / Forterre, P.
History
DepositionJun 14, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UP1
B: UP1
C: UP1
D: UP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,70615
Polymers144,9794
Non-polymers2,72611
Water45025
1
A: UP1
B: UP1
hetero molecules

A: UP1
B: UP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,95316
Polymers144,9794
Non-polymers2,97412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area5810 Å2
ΔGint-5 kcal/mol
Surface area64150 Å2
MethodPQS
2
C: UP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9884
Polymers36,2451
Non-polymers7443
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
D: UP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7413
Polymers36,2451
Non-polymers4962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)89.824, 230.305, 81.968
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
UP1


Mass: 36244.828 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROCOCCUS ABYSSI (archaea) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA (DE3) PLYSS / References: UniProt: Q9UXT7
#2: Chemical
ChemComp-WO4 / TUNGSTATE(VI)ION


Mass: 247.838 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: WO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 3.01 Å3/Da / Density % sol: 58.75 %
Crystal growpH: 5.6 / Details: pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.2145
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2145 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 38457 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 9.9 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 21.7
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 9.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→20 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.868 / SU B: 14.533 / SU ML: 0.276 / Cross valid method: THROUGHOUT / ESU R Free: 0.389 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1916 5 %RANDOM
Rwork0.202 ---
obs0.204 36494 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20 Å2
2---1.86 Å20 Å2
3---1.43 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9996 0 55 25 10076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02210216
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1541.98113794
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.19351296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59523.113424
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.721151796
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8081580
X-RAY DIFFRACTIONr_chiral_restr0.0710.21575
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027556
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.24484
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.27067
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.2257
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.273
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2370.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4971.56568
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.872210252
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.07134021
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8284.53542
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.97 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.376 138
Rwork0.286 2594

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