[English] 日本語
Yorodumi
- PDB-5c4q: Crystal Structure Analysis of bromodomain from Leishmania donovan... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5c4q
TitleCrystal Structure Analysis of bromodomain from Leishmania donovani complexed with bromosporine
ComponentsBromodomain
KeywordsTRANSCRIPTION / Structural Genomics Consortium / SGC / Bromodomain / Bromosporine / Leishmania donovani
Function / homology
Function and homology information


: / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bromosporine / Bromodomain factor 2 protein, putative
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.932 Å
AuthorsJiang, D.Q. / Tempel, W. / Loppnau, P. / Graslund, S. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / Amani, M. / Hou, C.F.D. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal Structure Analysis of bromodomain from Leishmania donovani complexed with bromosporine
Authors: Jiang, D.Q. / Tempel, W. / Loppnau, P. / Graslund, S. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / Amani, M. / Hou, C.F.D.
History
DepositionJun 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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
B: Bromodomain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,69013
Polymers28,8812
Non-polymers80911
Water2,522140
1
A: Bromodomain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8456
Polymers14,4401
Non-polymers4045
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8457
Polymers14,4401
Non-polymers4046
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-6 kcal/mol
Surface area12530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.916, 34.385, 86.463
Angle α, β, γ (deg.)90.000, 117.580, 90.000
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly of the protein indicated by Mass spectrometry and Gel filtration is monomer.

-
Components

#1: Protein Bromodomain


Mass: 14440.311 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (strain BPK282A1) (eukaryote)
Strain: BPK282A1 / Gene: LDBPK_363130 / Plasmid: V3R pRARE2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E9BU22
#2: 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.: 2 / Source method: obtained synthetically / Formula: C17H20N6O4S
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 9 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.03 Å3/Da / Density % sol: 39.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.4 M sodium malonate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→20 Å / Num. obs: 16741 / % possible obs: 94.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 23.97 Å2 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.055 / Rrim(I) all: 0.109 / Χ2: 1.524 / Net I/av σ(I): 14.418 / Net I/σ(I): 7.2 / Num. measured all: 61331
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.93-1.9620.4455380.7560.3290.5570.67661.6
1.96-22.30.3866440.7890.2780.4790.70672.6
2-2.042.70.3797020.8520.2530.4590.67282
2.04-2.082.90.3377730.8840.2160.4030.6990
2.08-2.123.20.3228470.8840.20.3810.73495.1
2.12-2.173.50.3298460.9260.1970.3851.47397.1
2.17-2.233.70.2498530.9430.1480.290.75599.6
2.23-2.293.80.238950.950.1340.2670.85599.6
2.29-2.3640.2328550.9530.1340.2680.88999.8
2.36-2.4340.1978930.9580.1140.2290.944100
2.43-2.5240.1688610.970.0960.1940.84799.8
2.52-2.6240.1619030.9730.0930.1860.966100
2.62-2.7440.1428570.9820.0810.1640.976100
2.74-2.8840.1168750.9850.0660.1351.147100
2.88-3.0640.0988850.9890.0560.1141.298100
3.06-3.340.088870.9880.0450.0921.973100
3.3-3.6340.0668870.9880.0380.0772.595100
3.63-4.1540.0628980.990.0360.0723.432100
4.15-5.2140.0529080.9960.0290.062.898100
5.21-203.80.0559340.9960.0320.0633.43299.5

-
Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HBW

4hbw


Resolution: 1.932→19.16 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.06 / Stereochemistry target values: ML
Details: Bromosporine restraints generated by PHENIX.ELBOW were modified to restrain coordinates of the lactamate moiety in a single plane, prompted by a MOGUL query of related structures in the ...Details: Bromosporine restraints generated by PHENIX.ELBOW were modified to restrain coordinates of the lactamate moiety in a single plane, prompted by a MOGUL query of related structures in the Cambridge Structural Database.
RfactorNum. reflection% reflection
Rfree0.2398 802 4.79 %
Rwork0.1814 15936 -
obs0.1842 16738 94.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.05 Å2 / Biso mean: 23.9427 Å2 / Biso min: 10.67 Å2
Refinement stepCycle: final / Resolution: 1.932→19.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1826 0 91 140 2057
Biso mean--26.04 28 -
Num. residues----232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121971
X-RAY DIFFRACTIONf_angle_d1.0322691
X-RAY DIFFRACTIONf_chiral_restr0.037287
X-RAY DIFFRACTIONf_plane_restr0.005339
X-RAY DIFFRACTIONf_dihedral_angle_d14.493698
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9324-2.05340.3057990.23641990208972
2.0534-2.21170.27511210.20032674279596
2.2117-2.43390.25611360.191827902926100
2.4339-2.78510.28561760.201527602936100
2.7851-3.50550.26991300.180128182948100
3.5055-19.16060.17461400.158129043044100

+
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