[English] 日本語
Yorodumi
- PDB-6nim: Trypanosoma cruzi - BDF2, TcCLB.506553.20, solved with bromosporine -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nim
TitleTrypanosoma cruzi - BDF2, TcCLB.506553.20, solved with bromosporine
ComponentsBromodomain factor 2 protein
KeywordsSIGNALING PROTEIN / TcCLB.506553.20 / BDF2 / bromosporine / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


: / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily ...: / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bromosporine / Bromodomain factor 2 protein
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.78 Å
AuthorsLin, Y.H. / Dong, A. / Tempel, W. / Loppnau, P. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Hui, R. / Vedadi, M. / Harding, R. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Trypanosoma cruzi - BDF2, TcCLB.506553.20, solved with bromosporine
Authors: Lin, Y.H. / Dong, A. / Tempel, W. / Loppnau, P. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Hui, R. / Vedadi, M. / Harding, R. / Structural Genomics Consortium (SGC)
History
DepositionDec 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bromodomain factor 2 protein
B: Bromodomain factor 2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,02512
Polymers27,2372
Non-polymers78910
Water3,387188
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-42 kcal/mol
Surface area11870 Å2
Unit cell
Length a, b, c (Å)68.999, 65.784, 60.107
Angle α, β, γ (deg.)90.000, 110.640, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-206-

UNX

-
Components

#1: Protein Bromodomain factor 2 protein


Mass: 13618.282 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: C4B63_57g96 / Plasmid: pET15-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-pRARE2 / References: UniProt: A0A2V2V5V1
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 5 / Source method: obtained synthetically
#4: Chemical ChemComp-BMF / Bromosporine / ethyl (3-methyl-6-{4-methyl-3-[(methylsulfonyl)amino]phenyl}[1,2,4]triazolo[4,3-b]pyridazin-8-yl)carbamate


Mass: 404.444 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N6O4S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.51 % / Mosaicity: 0.985 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 2.0 M NH4SO4 and 0.1M bis Tris pH5.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Nov 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 23959 / % possible obs: 98.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.03 / Rrim(I) all: 0.061 / Χ2: 1.035 / Net I/σ(I): 11.3 / Num. measured all: 91630
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.78-1.812.90.45310120.820.2860.5390.89785.6
1.81-1.843.20.37211590.9120.230.440.8195.2
1.84-1.883.50.37411680.8850.2260.4390.81398.4
1.88-1.923.70.2912080.9210.1710.3380.84199.8
1.92-1.963.80.26411980.9410.1540.3070.87799.5
1.96-23.90.21312180.9450.1250.2480.88399.8
2-2.053.90.16911920.970.0980.1960.866100
2.05-2.113.90.14911920.980.0860.1720.95499.9
2.11-2.173.90.11912440.9820.0690.1380.896100
2.17-2.243.90.10111810.9890.0580.1170.952100
2.24-2.323.90.09512170.990.0550.110.992100
2.32-2.4240.08112110.9920.0470.0940.975100
2.42-2.5340.07412200.9930.0420.0851.043100
2.53-2.6640.06712180.9940.0390.0771.108100
2.66-2.8340.05611960.9960.0320.0651.081100
2.83-3.0440.04512100.9970.0260.0521.051100
3.04-3.3540.03812260.9980.0220.0441.071100
3.35-3.8340.03112220.9980.0180.0361.164100
3.83-4.8340.03112200.9990.0180.0361.355100
4.83-503.80.03712470.9980.0220.0431.84898.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.76 Å21.7 Å
Translation2.76 Å21.7 Å

-
Processing

Software
NameVersionClassification
HKL-3000data scaling
PHASER2.8.2phasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CZG

5czg


Resolution: 1.78→21.71 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.561 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.112
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2044 935 4 %RANDOM
Rwork0.1703 ---
obs0.1717 22496 97.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 78.08 Å2 / Biso mean: 23.223 Å2 / Biso min: 14.41 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å20 Å2-0.09 Å2
2--0.25 Å20 Å2
3---0.76 Å2
Refinement stepCycle: final / Resolution: 1.78→21.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1769 0 53 191 2013
Biso mean--42.38 34.13 -
Num. residues----226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131874
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171607
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.6282557
X-RAY DIFFRACTIONr_angle_other_deg1.4971.5823720
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7535228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.05223.654104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.52215284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.554158
X-RAY DIFFRACTIONr_chiral_restr0.0730.2234
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022161
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02390
LS refinement shellResolution: 1.782→1.828 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 53 -
Rwork0.302 1398 -
all-1451 -
obs--81.93 %

+
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