[English] 日本語
Yorodumi
- PDB-7a28: Crystal structure of T. brucei PDE-B1 catalytic domain with inhib... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7a28
TitleCrystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-617
ComponentsPhosphodiesterase
KeywordsHYDROLASE / Parasitic phosphodiesterase / African trypanosomiasis / sleeping sickness
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / axoneme / 3',5'-cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / cell morphogenesis / signal transduction / metal ion binding / cytoplasm
Similarity search - Function
3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase, conserved site / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase domain signature. / 3'5'-cyclic nucleotide phosphodiesterase domain profile. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain ...3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase, conserved site / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase domain signature. / 3'5'-cyclic nucleotide phosphodiesterase domain profile. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain
Similarity search - Domain/homology
GUANIDINE / DI(HYDROXYETHYL)ETHER / Chem-QWT / Phosphodiesterase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsSingh, A.K. / Blaazer, A.R. / Zara, L. / de Esch, I.J.P. / Leurs, R. / Brown, D.G.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)602666European Union
CitationJournal: To be published
Title: Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-617
Authors: Singh, A.K. / Brown, D.G.
History
DepositionAug 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphodiesterase
B: Phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,79223
Polymers81,2472
Non-polymers2,54521
Water8,179454
1
A: Phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,11014
Polymers40,6231
Non-polymers1,48613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6829
Polymers40,6231
Non-polymers1,0598
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.990, 116.530, 69.150
Angle α, β, γ (deg.)90.000, 108.580, 90.000
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Phosphodiesterase


Mass: 40623.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: residues 565-918 / Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: PDEB1 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): codon plus
References: UniProt: Q8WQX9, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases

-
Non-polymers , 7 types, 475 molecules

#2: Chemical ChemComp-QWT / 1-cycloheptyl-3-(4-methoxy-3-{4-[4-(1H-1,2,3,4-tetrazol-5-yl)phenoxy]butoxy}phenyl)-4,4-dimethyl-4,5-dihydro-1H-pyrazol-5-one / 2-cycloheptyl-5-[4-methoxy-3-[4-[4-(1~{H}-1,2,3,4-tetrazol-5-yl)phenoxy]butoxy]phenyl]-4,4-dimethyl-pyrazol-3-one


Mass: 546.661 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H38N6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-GAI / GUANIDINE


Mass: 59.070 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH5N3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 3350, 0.4 M sodium formate, 0.3 M guanidine, 0.1 M MES pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.89→80.33 Å / Num. obs: 69296 / % possible obs: 98.8 % / Redundancy: 3.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.053 / Rrim(I) all: 0.1 / Net I/σ(I): 10.3
Reflection shellResolution: 1.89→1.94 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.289 / Num. unique obs: 5104 / CC1/2: 0.476 / Rpim(I) all: 0.83 / Rrim(I) all: 1.539 / % possible all: 98.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I15

4i15


Resolution: 1.89→80.33 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 4.623 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2023 3342 4.8 %RANDOM
Rwork0.1743 ---
obs0.1756 65953 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 118.73 Å2 / Biso mean: 35.511 Å2 / Biso min: 11.43 Å2
Baniso -1Baniso -2Baniso -3
1-3.32 Å20 Å20.08 Å2
2---1.04 Å20 Å2
3----1.9 Å2
Refinement stepCycle: final / Resolution: 1.89→80.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5260 0 154 454 5868
Biso mean--54.75 43.8 -
Num. residues----665
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135503
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175119
X-RAY DIFFRACTIONr_angle_refined_deg1.5751.6387422
X-RAY DIFFRACTIONr_angle_other_deg1.3781.59111837
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5225663
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.87122.466292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.88915933
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5941535
X-RAY DIFFRACTIONr_chiral_restr0.0840.2703
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026258
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021167
LS refinement shellResolution: 1.89→1.939 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 254 -
Rwork0.349 4840 -
all-5094 -
obs--98.76 %

+
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