[English] 日本語
Yorodumi
- PDB-7amh: SmBRD3(2), Second Bromodomain of Bromodomain 3 from Schistosoma m... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7amh
TitleSmBRD3(2), Second Bromodomain of Bromodomain 3 from Schistosoma mansoni in complex with DM-A-33, an iBET726 analogue
ComponentsPutative bromodomain-containing protein 3, brd3
KeywordsPROTEIN BINDING / bromo domain / methyllysine binding / epigenetic reader domain / inhibitor / complex
Function / homology
Function and homology information


NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain ...NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
Chem-RN5 / Putative bromodomain-containing protein 3, brd3
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.863 Å
AuthorsMcArdle, D. / Schiedel, M. / McDonough, M.A. / Conway, S.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S507015/1 United Kingdom
CitationJournal: To Be Published
Title: SBM3_2, Second Bromodomain of Bromodomain 3 from Schistosoma mansoni in complex with DM1, an iBET726 analogue
Authors: McArdle, D.J.B. / Schiedel, M. / McDonough, M.A. / Conway, S.J.
History
DepositionOct 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative bromodomain-containing protein 3, brd3
B: Putative bromodomain-containing protein 3, brd3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9734
Polymers30,0602
Non-polymers9132
Water3,729207
1
A: Putative bromodomain-containing protein 3, brd3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4862
Polymers15,0301
Non-polymers4571
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative bromodomain-containing protein 3, brd3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4862
Polymers15,0301
Non-polymers4571
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.201, 84.111, 126.736
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-387-

HOH

-
Components

#1: Protein Putative bromodomain-containing protein 3, brd3


Mass: 15029.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5K4EQL3
#2: Chemical ChemComp-RN5 / 4-{(2S, 4R)-1-acetyl-4-[(1-benzothiophen-6-yl)amino]-2-methyl-1,2,3,4-tetrahydroquinolin-6-yl}benzoic acid / 4-[(2~{S},4~{R})-4-(1-benzothiophen-6-ylamino)-1-ethanoyl-2-methyl-3,4-dihydro-2~{H}-quinolin-6-yl]benzoic acid


Mass: 456.556 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H24N2O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium dihydrogen Phosphate monohydrate, 20% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9119 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9119 Å / Relative weight: 1
ReflectionResolution: 1.863→63.368 Å / Num. obs: 42925 / % possible obs: 99.9 % / Redundancy: 11.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.227 / Rpim(I) all: 0.069 / Rrim(I) all: 0.237 / Net I/σ(I): 6.8
Reflection shellResolution: 1.863→1.895 Å / Rmerge(I) obs: 4.369 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 2292 / CC1/2: 0.47 / Rpim(I) all: 1.506 / Rrim(I) all: 4.632

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHENIX1.14refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AMC

7amc


Resolution: 1.863→63.368 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2505 2157 5.03 %
Rwork0.2174 40768 -
obs0.2191 42925 95.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.08 Å2 / Biso mean: 40.8409 Å2 / Biso min: 17.44 Å2
Refinement stepCycle: final / Resolution: 1.863→63.368 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1821 0 112 210 2143
Biso mean--37.98 40.04 -
Num. residues----226
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.863-1.90630.4317920.3752174761
1.9063-1.9540.38811150.3514231382
1.954-2.00690.33631140.3399260889
2.0069-2.06590.3571200.3202285899
2.0659-2.13260.30971650.29012792100
2.1326-2.20880.27941560.26152835100
2.2088-2.29730.30331610.2485281299
2.2973-2.40180.25541630.23152858100
2.4018-2.52850.22681580.21832839100
2.5285-2.68690.23281420.20542864100
2.6869-2.89430.25961570.20872857100
2.8943-3.18560.23591670.19982818100
3.1856-3.64650.23051230.18812872100
3.6465-4.5940.22861650.16552850100
4.594-63.3680.22051590.21092845100
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)
16.3506-1.1316-3.48238.7532.88934.35260.0262-0.26520.73690.23160.54-1.2617-0.0161.8117-0.47390.306-0.1342-0.010.6099-0.03790.486443.307473.998438.404
28.0487-3.13010.56867.3654.18223.19990.0187-0.93521.26760.51410.0984-0.8668-0.25990.6744-0.03990.4763-0.2401-0.01610.5758-0.09940.48734.092780.484350.6346
33.14481.0145-3.15554.2985-2.35398.7108-0.0476-0.1088-0.21110.10930.0475-0.11960.21170.2442-0.03410.15050.03290.00330.1879-0.0150.18922.424165.340748.5836
47.8601-1.3751-4.6411.69440.50035.28080.02510.2331-0.0979-0.1474-0.0494-0.1794-0.20370.40150.03010.2407-0.0457-0.01940.2878-0.03090.180231.506368.827138.7866
57.54432.0615-6.01582.6212-1.89478.4450.28640.33440.3912-0.2616-0.1007-0.2345-0.8745-0.1496-0.28070.4976-0.0390.01140.18160.03950.292428.382379.986639.225
67.43771.8473.02887.836-0.35162.34570.08180.6594-0.8499-0.7724-0.13060.63220.46020.060.07790.3975-0.0319-0.02350.3119-0.08020.339331.786846.117645.1033
76.78920.83291.72377.6334.48542.90370.02960.0274-0.2067-0.54690.624-0.73160.57090.6855-0.55310.3843-0.00360.00950.3035-0.01580.372745.563347.378954.3218
82.51180.78792.28212.17982.89248.88790.1572-0.0508-0.11270.1583-0.2540.20590.4441-0.73980.11050.1858-0.0775-0.00850.36850.00060.24832.846151.067365.4528
94.21231.27634.09840.98741.61128.35990.0856-0.22720.02-0.008-0.23430.2908-0.0172-0.92780.22720.21040.0567-0.02160.4178-0.02630.261629.122255.664155.1331
109.24531.86614.73155.00210.94453.56140.20440.2756-0.0472-0.2019-0.2380.095-0.13620.14250.06650.25530.04220.03820.2770.00450.238838.212357.622451.0755
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 31 )A15 - 31
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 40 )A32 - 40
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 66 )A41 - 66
4X-RAY DIFFRACTION4chain 'A' and (resid 67 through 100 )A67 - 100
5X-RAY DIFFRACTION5chain 'A' and (resid 101 through 127 )A101 - 127
6X-RAY DIFFRACTION6chain 'B' and (resid 16 through 31 )B16 - 31
7X-RAY DIFFRACTION7chain 'B' and (resid 32 through 40 )B32 - 40
8X-RAY DIFFRACTION8chain 'B' and (resid 41 through 75 )B41 - 75
9X-RAY DIFFRACTION9chain 'B' and (resid 76 through 100 )B76 - 100
10X-RAY DIFFRACTION10chain 'B' and (resid 101 through 128 )B101 - 128

+
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://pdbjlc1.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