[English] 日本語
- PDB-5n29: An improved model of the Trypanosoma brucei CTP synthase glutamin... -

Open data

ID or keywords:


Basic information

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

CTP synthase activity / CTP synthase (glutamine hydrolysing) / 'de novo' CTP biosynthetic process / glutamine metabolic process / ATP binding
Similarity search - Function
CTP synthase / CTP synthase GATase domain / CTP synthase, N-terminal / CTP synthase N-terminus / Glutamine amidotransferase type 1 domain profile. / Glutamine amidotransferase class-I / Glutamine amidotransferase / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / P-loop containing nucleoside triphosphate hydrolase ...CTP synthase / CTP synthase GATase domain / CTP synthase, N-terminal / CTP synthase N-terminus / Glutamine amidotransferase type 1 domain profile. / Glutamine amidotransferase class-I / Glutamine amidotransferase / 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 (unknown)
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.
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

Structure visualization

Structure viewerMolecule:

Downloads & links


Deposited unit
A: CTP synthase
hetero molecules

Theoretical massNumber of molelcules
Total (without water)30,8694

  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-34 kcal/mol
Surface area12190 Å2
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


#1: Protein CTP synthase / CTP synthetase / 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) (unknown)
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 / Chloride

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

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

Experimental details


ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 38.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop

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


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_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_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 %

About Yorodumi


Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive


Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more