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- PDB-2ivn: Structure of UP1 protein -

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Basic information

Entry
Database: PDB / ID: 2ivn
TitleStructure of UP1 protein
ComponentsO-SIALOGLYCOPROTEIN ENDOPEPTIDASE
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / tRNA N6-adenosine threonylcarbamoyltransferase
Similarity search - Component
Biological speciesPYROCOCCUS ABYSSI (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 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
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: O-SIALOGLYCOPROTEIN ENDOPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8674
Polymers36,2451
Non-polymers6233
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)61.933, 69.868, 75.723
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 O-SIALOGLYCOPROTEIN ENDOPEPTIDASE / UP1 / GLOCOPROTEASE


Mass: 36244.828 Da / Num. of mol.: 1
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, EC: 3.4.24.57
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.14 Å3/Da / Density % sol: 41.95 % / Description: NONE
Crystal growpH: 5.6 / Details: 25% PEG 4000, 0.3M KCL, 0.1M SODIUM CITRATE PH5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. obs: 41853 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 25.1
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 2.84 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.65→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.029 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1987 5 %RANDOM
Rwork0.212 ---
obs0.213 37910 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å20 Å2
2---0.51 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2499 0 38 203 2740
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222581
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9871.9933489
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7345324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.70723.113106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.39715449
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7491520
X-RAY DIFFRACTIONr_chiral_restr0.0570.2395
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021900
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1650.21237
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2940.21801
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0780.2174
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1010.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0760.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3081.51662
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.51822563
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.8631045
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.4114.5926
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: 1.65→1.69 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.354 157
Rwork0.307 2767

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