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- PDB-2v4u: Human CTP synthetase 2 - glutaminase domain in complex with 5-OXO... -

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Basic information

Entry
Database: PDB / ID: 2v4u
TitleHuman CTP synthetase 2 - glutaminase domain in complex with 5-OXO-L- NORLEUCINE
ComponentsCTP SYNTHASE 2
KeywordsLIGASE / PYRIMIDINE BIOSYNTHESIS / GLUTAMINE AMIDOTRANSFERASE / GLUTAMINASE DOMAIN / 5-OXO-L-NORLEUCINE / DON / CTPS / PHOSPHOPROTEIN / CTP SYNTHETASE / CYTIDINE 5'- TRIPHOSPHATE SYNTHETASE 2 / NUCLEOTIDE METABOLISM / UTP-- AMMONIA LIGASE 2
Function / homology
Function and homology information


cytoophidium / CTP synthase (glutamine hydrolysing) / CTP synthase activity / pyrimidine nucleotide metabolic process / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / Interconversion of nucleotide di- and triphosphates / CTP biosynthetic process / glutamine metabolic process / ATP binding ...cytoophidium / CTP synthase (glutamine hydrolysing) / CTP synthase activity / pyrimidine nucleotide metabolic process / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / Interconversion of nucleotide di- and triphosphates / CTP biosynthetic process / glutamine metabolic process / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
CTP synthase / CTP synthase, N-terminal / CTP synthase GATase domain / CTP synthase N-terminus / Glutamine amidotransferase / Glutamine amidotransferase class-I / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold ...CTP synthase / CTP synthase, N-terminal / CTP synthase GATase domain / CTP synthase N-terminus / Glutamine amidotransferase / Glutamine amidotransferase class-I / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWelin, M. / Moche, M. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. ...Welin, M. / Moche, M. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Lehtio, L. / Nilsson, M.E. / Nyman, T. / Olesen, K. / Persson, C. / Sagemark, J. / Schueler, H. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Wisniewska, M. / Weigelt, J. / Wikstrom, M. / Nordlund, P.
CitationJournal: To be Published
Title: Human Ctp Synthetase 2 - Glutaminase Domain in Complex with 5-Oxo-L-Norleucine
Authors: Welin, M. / Moche, M. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, ...Authors: Welin, M. / Moche, M. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Lehtio, L. / Nilsson, M.E. / Nyman, T. / Olesen, K. / Persson, C. / Sagemark, J. / Schueler, H. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Wisniewska, M. / Weigelt, J. / Wikstrom, M. / Nordlund, P.
History
DepositionSep 29, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CTP SYNTHASE 2


Theoretical massNumber of molelcules
Total (without water)32,7671
Polymers32,7671
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)118.880, 72.330, 41.470
Angle α, β, γ (deg.)90.00, 95.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CTP SYNTHASE 2 / UTP--AMMONIA LIGASE 2 / CTP SYNTHETASE 2


Mass: 32766.756 Da / Num. of mol.: 1 / Fragment: GLUTAMINASE DOMAIN, RESIDUES 297-562
Source method: isolated from a genetically manipulated source
Details: CYS399 IS COVALENTLY MODIFIED WITH 5-OXO-L-NORLEUCINE
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3
References: UniProt: Q9NRF8, CTP synthase (glutamine hydrolysing)
#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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.9 % / Description: NONE
Crystal growpH: 7
Details: 0.1M HEPES, PH 7.0, 0.02 M MGCL2, 30% POLYACRYLIC ACID 5100. CRYSTALS WERE SOAKED WITH 20.6 MM DON FOR 90 MIN

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 21, 2008 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 15010 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 18.27
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 11.3 / % possible all: 86.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VKT

2vkt


Resolution: 2.3→19.72 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.915 / SU B: 6.611 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.309 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1050 7 %RANDOM
Rwork0.207 ---
obs0.211 13946 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: 31.91 Å2
Baniso -1Baniso -2Baniso -3
1-2.07 Å20 Å2-2.11 Å2
2---1.81 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2107 0 0 40 2147
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222154
X-RAY DIFFRACTIONr_bond_other_d0.0020.021500
X-RAY DIFFRACTIONr_angle_refined_deg1.2661.9772913
X-RAY DIFFRACTIONr_angle_other_deg1.4723.0023645
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1525266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.83323.89595
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04315376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.281514
X-RAY DIFFRACTIONr_chiral_restr0.0710.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022375
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02425
X-RAY DIFFRACTIONr_nbd_refined0.1890.2400
X-RAY DIFFRACTIONr_nbd_other0.180.21564
X-RAY DIFFRACTIONr_nbtor_refined0.1680.21017
X-RAY DIFFRACTIONr_nbtor_other0.0960.21144
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.260
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2660.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.220.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8281.51482
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2322144
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4923888
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1424.5769
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: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.431 61
Rwork0.267 807

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