[English] 日本語
Yorodumi
- PDB-9hhb: Crystal Structure of the Plasmodium vivax Bromodomain PvBDP1 in c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9hhb
TitleCrystal Structure of the Plasmodium vivax Bromodomain PvBDP1 in complex with RMM21
ComponentsBromo domain-containing protein
KeywordsTRANSCRIPTION / plasmodium / bromodomain / inhibitor / complex
Function / homology
Function and homology information


Ankyrin repeats (many copies) / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Bromodomain, conserved site / Bromodomain signature. / Bromodomain ...Ankyrin repeats (many copies) / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
: / Bromo domain-containing protein
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsAmann, M. / Huegle, M. / Einsle, O. / Guenther, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)RTG2202 Germany
CitationJournal: Chemmedchem / Year: 2025
Title: A Novel Inhibitor against the Bromodomain Protein 1 of the Malaria Pathogen Plasmodium Falciparum.
Authors: Amann, M. / Warstat, R. / Rechten, K.K. / Theuer, P. / Schustereder, M. / Clavey, S. / Breit, B. / Einsle, O. / Hugle, M. / Petter, M. / Gunther, S.
History
DepositionNov 21, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2025Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jun 11, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bromo domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6063
Polymers15,1631
Non-polymers4432
Water99155
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-6 kcal/mol
Surface area7030 Å2
Unit cell
Length a, b, c (Å)92.382, 92.382, 69.811
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-345-

HOH

21A-350-

HOH

31A-355-

HOH

-
Components

#1: Protein Bromo domain-containing protein


Mass: 15163.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Gene: PVX_111040 / Production host: Escherichia coli (E. coli) / References: UniProt: A5KDW3
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-A1IUY / ~{N}-[2-methyl-3-(3-methyl-4-oxidanylidene-5,6,7,8-tetrahydro-2~{H}-cyclohepta[c]pyrrol-1-yl)phenyl]methanesulfonamide


Mass: 346.444 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H22N2O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.84 Å3/Da / Density % sol: 56.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 35% PEG3350, 0.4 M LiSO4, Tris pH 8,2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999987 Å / Relative weight: 1
ReflectionResolution: 2.26→46.19 Å / Num. obs: 8689 / % possible obs: 100 % / Redundancy: 38.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.023 / Rrim(I) all: 0.139 / Χ2: 1 / Net I/σ(I): 20 / Num. measured all: 333586
Reflection shellResolution: 2.26→2.33 Å / % possible obs: 100 % / Redundancy: 40.8 % / Rmerge(I) obs: 0.965 / Num. measured all: 31733 / Num. unique obs: 778 / CC1/2: 0.975 / Rpim(I) all: 0.153 / Rrim(I) all: 0.977 / Χ2: 1.02 / Net I/σ(I) obs: 5.6

-
Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→46.19 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2687 428 4.95 %
Rwork0.2163 --
obs0.2187 8653 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.26→46.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms952 0 29 55 1036
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021044
X-RAY DIFFRACTIONf_angle_d0.3761427
X-RAY DIFFRACTIONf_dihedral_angle_d19.235371
X-RAY DIFFRACTIONf_chiral_restr0.034150
X-RAY DIFFRACTIONf_plane_restr0.001179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.590.33951380.29442661X-RAY DIFFRACTION100
2.59-3.260.28951600.2662672X-RAY DIFFRACTION100
3.26-46.190.23681300.18142892X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 25.5415 Å / Origin y: -22.8954 Å / Origin z: -0.8998 Å
111213212223313233
T0.3414 Å20.0014 Å20.0181 Å2-0.2695 Å20.0032 Å2--0.6341 Å2
L2.4685 °21.2431 °21.0309 °2-2.0131 °21.2405 °2--4.0438 °2
S0.0924 Å °-0.083 Å °0.1185 Å °0.1775 Å °-0.0217 Å °0.0519 Å °-0.0414 Å °0.0164 Å °-0.0642 Å °
Refinement TLS groupSelection details: all

+
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