[English] 日本語
Yorodumi
- PDB-8rhx: Crystal Structure of Trypanosoma brucei PTR1 in complex with the ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8rhx
TitleCrystal Structure of Trypanosoma brucei PTR1 in complex with the cofactor and inhibitor P32
ComponentsPteridine reductase
KeywordsOXIDOREDUCTASE / Trypanosoma brucei / PTR1 / Pteridine reductase / cofactor / NADPH / inhibitor
Function / homology
Function and homology information


pteridine reductase activity / nucleotide binding
Similarity search - Function
Pteridine reductase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / ACETATE ION / Chem-NDP / Pteridine reductase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsPozzi, C. / Mangani, S. / Landi, G.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)CA21111European Union
CitationJournal: Acs Infect Dis. / Year: 2024
Title: Identification of Innovative Folate Inhibitors Leveraging the Amino Dihydrotriazine Motif from Cycloguanil for Their Potential as Anti- Trypanosoma brucei Agents.
Authors: Francesconi, V. / Rizzo, M. / Pozzi, C. / Tagliazucchi, L. / Konchie Simo, C.U. / Saporito, G. / Landi, G. / Mangani, S. / Carbone, A. / Schenone, S. / Santarem, N. / Tavares, J. / Cordeiro- ...Authors: Francesconi, V. / Rizzo, M. / Pozzi, C. / Tagliazucchi, L. / Konchie Simo, C.U. / Saporito, G. / Landi, G. / Mangani, S. / Carbone, A. / Schenone, S. / Santarem, N. / Tavares, J. / Cordeiro-da-Silva, A. / Costi, M.P. / Tonelli, M.
History
DepositionDec 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pteridine reductase
B: Pteridine reductase
C: Pteridine reductase
D: Pteridine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,33915
Polymers123,2044
Non-polymers4,13511
Water13,529751
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20310 Å2
ΔGint-131 kcal/mol
Surface area32510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.097, 89.431, 84.074
Angle α, β, γ (deg.)90.00, 115.95, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Pteridine reductase


Mass: 30800.982 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: PTR1 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O76290
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-A1H0T / 1-[4,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]guanidine


Mass: 244.081 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H7Cl2N5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 751 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.4 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 1.6-2.5 M sodium acetate and 0.1 M sodium citrate, pH 5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 22, 2023
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.48→66.63 Å / Num. obs: 163650 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 19 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.038 / Rrim(I) all: 0.061 / Net I/σ(I): 12.5
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 7985 / CC1/2: 0.867 / Rpim(I) all: 0.461 / Rrim(I) all: 0.726 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→66.63 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.257 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.18565 8195 5 %RANDOM
Rwork0.1631 ---
obs0.16426 155395 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.159 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2--0 Å20 Å2
3----0 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å
Refinement stepCycle: 1 / Resolution: 1.48→66.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7477 0 264 751 8492
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0128195
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.81911243
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.93351099
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.958574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.189101319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0970.21334
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026126
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.391.8564128
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.1443.3255160
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0152.0914067
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.40822.9513179
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: 1.48→1.518 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 613 -
Rwork0.279 11324 -
obs--99.63 %

+
About Yorodumi

-
News

-
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

-
Yorodumi

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