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- PDB-5n29: An improved model of the Trypanosoma brucei CTP synthase glutamin... -

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Basic information

Entry
Database: PDB / ID: 5n29
TitleAn improved model of the Trypanosoma brucei CTP synthase glutaminase domain:acivicin complex.
ComponentsCTP synthase
KeywordsLIGASE / CTP synthase
Function / homology
Function and homology information


CTP synthase (glutamine hydrolysing) / CTP synthase activity / 'de novo' CTP biosynthetic process / glutamine metabolic process / ATP binding
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 / P-loop containing nucleoside triphosphate hydrolase ...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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesTrypanosoma brucei gambiense (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
Authorsde Souza, J. / Dawson, A. / Hunter, W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
CitationJournal: J. Mol. Biol. / Year: 2010
Title: Crystal structure and comparative functional analyses of a Mycobacterium aldo-keto reductase.
Authors: Scoble, J. / McAlister, A.D. / Fulton, Z. / Troy, S. / Byres, E. / Vivian, J.P. / Brammananth, R. / Wilce, M.C. / Le Nours, J. / Zaker-Tabrizi, L. / Coppel, R.L. / Crellin, P.K. / Rossjohn, J. / Beddoe, T.
History
DepositionFeb 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2Jul 26, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0May 15, 2019Group: Data collection / Polymer sequence
Category: diffrn_source / entity_poly / pdbx_seq_map_depositor_info
Item: _diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_seq_map_depositor_info.one_letter_code
Revision 2.1Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 2.3Apr 9, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 0THIS ENTRY 5N29 REFLECTS AN ALTERNATIVE MODELING OF X-RAY DATA IN 2w7t.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CTP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8694
Polymers30,7621
Non-polymers1063
Water2,270126
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-34 kcal/mol
Surface area12190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.480, 63.680, 76.580
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 CTP synthase / UTP--ammonia ligase


Mass: 30762.158 Da / Num. of mol.: 1 / Mutation: H475Y
Source method: isolated from a genetically manipulated source
Details: Residue 419 is modified. This structure has been rerefined to improve the geometry of this modified residue.
Source: (gene. exp.) Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972) (eukaryote)
Strain: MHOM/CI/86/DAL972 / Gene: TbgDal_I580 / Plasmid: PNIC-BSA4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): R3 pRARE
References: UniProt: C9ZI73, CTP synthase (glutamine hydrolysing)
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.7 Å3/Da / Density % sol: 38.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: CRYSTALLIZATION CONDITIONS: 0.15 M POTASSIUM BROMIDE, 30 % PEG MONOMETHYL ETHER 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98004 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 11, 2008 / Details: Mirrors
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98004 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 14866 / % possible obs: 100 % / Redundancy: 7.84 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.9

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Processing

SoftwareName: REFMAC / Version: 5.8.0158 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.9 / SU B: 4.984 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.269 / ESU R Free: 0.2
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Acivicin is covalently bound to C419
RfactorNum. reflection% reflectionSelection details
Rfree0.23528 740 5 %RANDOM
Rwork0.19121 ---
obs0.19346 14087 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.877 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20 Å2
2--1.02 Å20 Å2
3----0.67 Å2
Refinement stepCycle: 1 / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2091 0 3 126 2220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192142
X-RAY DIFFRACTIONr_bond_other_d0.0020.021967
X-RAY DIFFRACTIONr_angle_refined_deg1.2321.9492889
X-RAY DIFFRACTIONr_angle_other_deg0.91234552
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.525262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.74223.654104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.96515363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6041517
X-RAY DIFFRACTIONr_chiral_restr0.0660.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022402
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02455
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1471.7941059
X-RAY DIFFRACTIONr_mcbond_other1.1461.7921058
X-RAY DIFFRACTIONr_mcangle_it1.9762.6871316
X-RAY DIFFRACTIONr_mcangle_other1.9752.691317
X-RAY DIFFRACTIONr_scbond_it1.2251.9941083
X-RAY DIFFRACTIONr_scbond_other1.2241.9881081
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0792.9051573
X-RAY DIFFRACTIONr_long_range_B_refined3.87621.3642369
X-RAY DIFFRACTIONr_long_range_B_other3.79221.322353
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 51 -
Rwork0.195 958 -
obs--93.34 %

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