[English] 日本語
Yorodumi
- PDB-5tcm: First Bromodomain from Leishmania donovani LdBPK.091320 complexed... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tcm
TitleFirst Bromodomain from Leishmania donovani LdBPK.091320 complexed with BI-2536
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / Bromodomain / Inhibitor / Structural Genomics Consortium (SGC)
Function / homology
Function and homology information


lysine-acetylated histone binding / regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain / Bromodomain profile. / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-R78 / Bromodomain family protein
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsLin, Y.H. / Hou, C.F.D. / Loppnau, P. / Dong, A. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Hui, R. / Walker, J.R. / Structural Genomics Consortium (SGC)
CitationJournal: To be published
Title: First Bromodomain from Leishmania donovani LdBPK.091320 complexed with BI-2536
Authors: Lin, Y.H. / Hou, C.F.D. / Loppnau, P. / Dong, A. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Hui, R. / Walker, J.R. / Structural Genomics Consortium (SGC)
History
DepositionSep 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / pdbx_struct_oper_list
Item: _audit_author.name / _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 18, 2018Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_detector ...chem_comp / diffrn_detector / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _diffrn_detector.detector ..._chem_comp.name / _diffrn_detector.detector / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7179
Polymers43,9663
Non-polymers1,7516
Water3,855214
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2393
Polymers14,6551
Non-polymers5842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3014
Polymers14,6551
Non-polymers6463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1772
Polymers14,6551
Non-polymers5221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.332, 85.250, 57.277
Angle α, β, γ (deg.)90.000, 94.460, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Uncharacterized protein


Mass: 14655.258 Da / Num. of mol.: 3 / Fragment: Bromodomain, UNP residues 8-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (strain BPK282A1) (eukaryote)
Strain: BPK282A1 / Gene: LDBPK_091320 / Plasmid: PET15-MHL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: E9BA17
#2: Chemical ChemComp-R78 / 4-{[(7R)-8-cyclopentyl-7-ethyl-5-methyl-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide


Mass: 521.654 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C28H39N7O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.8 Å3/Da / Density % sol: 61.25 % / Mosaicity: 0.836 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: The protein was crystallized at 293 K with 2M NaFormate, 0.1M BTP 7.0 and 1.0 M Cesium chloride with BI2536 using the sitting drop method.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9788 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 24639 / % possible obs: 99 % / Redundancy: 4.5 % / Biso Wilson estimate: 33.15 Å2 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.065 / Rrim(I) all: 0.148 / Χ2: 1.07 / Net I/av σ(I): 12.58 / Net I/σ(I): 4.8 / Num. measured all: 110927
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.2-2.244.30.5850.818197.2
2.24-2.284.40.5720.428199.2
2.28-2.324.50.4840.862198.8
2.32-2.374.60.4040.902199.2
2.37-2.424.60.380.924199.2
2.42-2.484.50.3480.924199.4
2.48-2.544.50.3340.93199.5
2.54-2.614.40.2860.942199.4
2.61-2.694.10.2490.914197.7
2.69-2.774.60.230.96199
2.77-2.874.70.2120.967199.4
2.87-2.994.70.170.973199.4
2.99-3.124.60.1460.981199.8
3.12-3.294.60.1290.982199.3
3.29-3.494.20.1120.98197.8
3.49-3.764.70.0970.988199.3
3.76-4.144.70.0850.991199.6
4.14-4.744.60.0760.993199.2
4.74-5.974.40.0710.992198.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASERphasing
BUSTER-TNT2.10.2refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TCK

5tck


Resolution: 2.2→44.05 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.901 / SU R Cruickshank DPI: 0.554 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.203 / SU Rfree Blow DPI: 0.169 / SU Rfree Cruickshank DPI: 0.169
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1246 5.09 %RANDOM
Rwork0.182 ---
obs0.184 24471 99 %-
Displacement parametersBiso max: 131.42 Å2 / Biso mean: 35.23 Å2 / Biso min: 12.39 Å2
Baniso -1Baniso -2Baniso -3
1--4.8884 Å20 Å24.5978 Å2
2--9.5417 Å20 Å2
3----4.6534 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: final / Resolution: 2.2→44.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2652 0 126 215 2993
Biso mean--43.1 40.25 -
Num. residues----346
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1254SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes67HARMONIC2
X-RAY DIFFRACTIONt_gen_planes920HARMONIC5
X-RAY DIFFRACTIONt_it5574HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion368SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6113SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5574HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg10000HARMONIC3.80.67
X-RAY DIFFRACTIONt_omega_torsion3.72
X-RAY DIFFRACTIONt_other_torsion14.47
LS refinement shellResolution: 2.2→2.3 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.219 133 4.48 %
Rwork0.185 2835 -
all-2968 -
obs--98.54 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.20030.9792-0.99591.9776-1.20622.15080.09020.03960.03930.0181-0.00160.1703-0.0591-0.1106-0.0886-0.02880.0434-0.0655-0.1040.0026-0.079916.029148.72059.8726
22.7136-0.4997-0.08780.92750.21760.6475-0.0062-0.019-0.08030.0466-0.01450.0521-0.0107-0.04280.02070.0002-0.0028-0.0375-0.0877-0.0146-0.097331.332441.718729.1219
30.9722-0.297-0.33111.80861.14432.51880.0752-0.0073-0.031-0.0240.00910.0192-0.0324-0.056-0.0844-0.012-0.0276-0.0554-0.12360.0207-0.058519.83423.766815.0749
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 116
2X-RAY DIFFRACTION2{ B|* }B2 - 116
3X-RAY DIFFRACTION3{ C|* }C2 - 116

+
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