[English] 日本語
Yorodumi
- PDB-5tpx: Bromodomain from Plasmodium Faciparum Gcn5, complexed with compound -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tpx
TitleBromodomain from Plasmodium Faciparum Gcn5, complexed with compound
ComponentsHistone acetyltransferase GCN5
KeywordsTRANSFERASE / Bromodomain / Structural Genomics Consortium (SGC)
Function / homology
Function and homology information


: / histone H3 acetyltransferase activity / histone acetyltransferase complex / chromatin remodeling / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Histone acetyltransferase GCN5 / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain profile. / bromo domain / Bromodomain ...Histone acetyltransferase GCN5 / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-7H7 / Histone acetyltransferase GCN5
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsLin, Y.H. / Hou, C.F.D. / MOUSTAKIM, M. / DIXON, D.J. / Loppnau, P. / Tempel, W. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Hui, R. ...Lin, Y.H. / Hou, C.F.D. / MOUSTAKIM, M. / DIXON, D.J. / Loppnau, P. / Tempel, W. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Hui, R. / BRENNAN, P.E. / Walker, J.R. / Structural Genomics Consortium (SGC)
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: Discovery of a PCAF Bromodomain Chemical Probe.
Authors: Moustakim, M. / Clark, P.G. / Trulli, L. / Fuentes de Arriba, A.L. / Ehebauer, M.T. / Chaikuad, A. / Murphy, E.J. / Mendez-Johnson, J. / Daniels, D. / Hou, C.D. / Lin, Y.H. / Walker, J.R. / ...Authors: Moustakim, M. / Clark, P.G. / Trulli, L. / Fuentes de Arriba, A.L. / Ehebauer, M.T. / Chaikuad, A. / Murphy, E.J. / Mendez-Johnson, J. / Daniels, D. / Hou, C.D. / Lin, Y.H. / Walker, J.R. / Hui, R. / Yang, H. / Dorrell, L. / Rogers, C.M. / Monteiro, O.P. / Fedorov, O. / Huber, K.V. / Knapp, S. / Heer, J. / Dixon, D.J. / Brennan, P.E.
History
DepositionOct 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Oct 4, 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: Histone acetyltransferase GCN5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4506
Polymers14,7661
Non-polymers6845
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.000, 75.000, 49.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-1502-

SO4

21A-1637-

HOH

-
Components

#1: Protein Histone acetyltransferase GCN5


Mass: 14765.800 Da / Num. of mol.: 1 / Fragment: Bromodomain (UNP residues 1356-1460)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PF3D7_0823300 / Plasmid: PET15-MHL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3)-pRARE2 / References: UniProt: Q8IB67, histone acetyltransferase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-7H7 / (1S,2S)-N~1~,N~1~-dimethyl-N~2~-(3-methyl[1,2,4]triazolo[3,4-a]phthalazin-6-yl)-1-phenylpropane-1,2-diamine


Mass: 360.455 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24N6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.36 Å3/Da / Density % sol: 47.94 % / Mosaicity: 1.537 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: The protein was crystallized at 293 K in 0.1M CaCl2, 30% PEG 8K, 0.2M NH4SO4 with 2mM compound using the sitting drop method.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98011 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Sep 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.1→37.55 Å / Num. obs: 8411 / % possible obs: 96 % / Redundancy: 7.8 % / Biso Wilson estimate: 38.07 Å2 / Rmerge(I) obs: 0.1 / Net I/av σ(I): 20.575 / Net I/σ(I): 6.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.1-2.147.80.7250.877189
2.14-2.187.70.7090.847189.4
2.18-2.227.60.6080.911198.6
2.22-2.267.80.4660.934195.3
2.26-2.317.80.440.9511100
2.31-2.377.90.4130.944196.7
2.37-2.427.90.340.956199.5
2.42-2.4980.3070.968196.3
2.49-2.567.80.2890.9661100
2.56-2.6580.2310.981196.4
2.65-2.747.80.2060.986198.1
2.74-2.857.90.170.993198.1
2.85-2.987.90.1350.992196.3
2.98-3.147.90.0970.995196.4
3.14-3.337.90.0780.998196.4
3.33-3.597.90.0750.997196.6
3.59-3.957.80.0810.995196.9
3.95-4.527.80.0650.997193.8
4.52-5.697.70.0520.997195.2
5.69-37.557.10.0560.998192.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
BUSTER-TNT2.10.2refinement
PDB_EXTRACT3.2data extraction
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
BUSTERrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QNS

4qns


Resolution: 2.1→37.5 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.911 / SU R Cruickshank DPI: 0.396 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.206 / SU Rfree Blow DPI: 0.18 / SU Rfree Cruickshank DPI: 0.173
RfactorNum. reflection% reflectionSelection details
Rfree0.236 390 4.66 %RANDOM
Rwork0.185 ---
obs0.188 8368 96.1 %-
Displacement parametersBiso max: 102.19 Å2 / Biso mean: 45.42 Å2 / Biso min: 26.88 Å2
Baniso -1Baniso -2Baniso -3
1-6.2745 Å20 Å20 Å2
2--6.2745 Å20 Å2
3----12.5489 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: final / Resolution: 2.1→37.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms870 0 43 66 979
Biso mean--54.2 48.99 -
Num. residues----106
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d392SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes23HARMONIC2
X-RAY DIFFRACTIONt_gen_planes280HARMONIC5
X-RAY DIFFRACTIONt_it1806HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion120SEMIHARMONIC5
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_contact2027SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1806HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3250HARMONIC3.80.67
X-RAY DIFFRACTIONt_omega_torsion3.7
X-RAY DIFFRACTIONt_other_torsion14.05
LS refinement shellResolution: 2.1→2.35 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.257 106 4.62 %
Rwork0.182 2188 -
all-2294 -
obs--94.95 %
Refinement TLS params.Method: refined / Origin x: 23.6336 Å / Origin y: 84.979 Å / Origin z: 57.9396 Å
111213212223313233
T-0.183 Å20.0118 Å20.0204 Å2--0.2053 Å2-0.0153 Å2---0.0498 Å2
L2.5974 °20.06 °2-0.0608 °2-1.9328 °2-0.2513 °2--1.8437 °2
S-0.0098 Å °-0.2411 Å °-0.0128 Å °0.2183 Å °-0.012 Å °0.1618 Å °-0.0784 Å °-0.0147 Å °0.0219 Å °
Refinement TLS groupSelection details: { A|* }

+
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://pdbjlvh1.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