[English] 日本語
Yorodumi
- PDB-9evq: Crystal structure of the kinetoplastid kinetochore protein KKT23 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9evq
TitleCrystal structure of the kinetoplastid kinetochore protein KKT23 acetyltransferase domain from Trypanosoma brucei
ComponentsN-acetyltransferase domain-containing protein
KeywordsCELL CYCLE / kinetochore / kinetoplastid / histone / acetyltransferase / mitosis
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / kinetochore / nucleus / cytoplasm
Similarity search - Function
Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
ACETYL COENZYME *A / N-acetyltransferase domain-containing protein
Similarity search - Component
Biological speciesTrypanosoma brucei brucei TREU927 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLudzia, P. / Ishii, M. / Akiyoshi, B.
Funding support United Kingdom, Germany, 2items
OrganizationGrant numberCountry
Wellcome Trust210622/Z/18/Z/WT United Kingdom
Boehringer Ingelheim Fonds (BIF) Germany
CitationJournal: Biorxiv / Year: 2024
Title: The kinetoplastid kinetochore protein KKT23 acetyltransferase is a structural homolog of GCN5 that acetylates the histone H2A C-terminal tail
Authors: Ludzia, P. / Ishii, M. / Akiyoshi, B.
History
DepositionApr 1, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: N-acetyltransferase domain-containing protein
A: N-acetyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8614
Polymers52,2422
Non-polymers1,6192
Water7,584421
1
B: N-acetyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9312
Polymers26,1211
Non-polymers8101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: N-acetyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9312
Polymers26,1211
Non-polymers8101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.266, 44.317, 68.815
Angle α, β, γ (deg.)100.508, 103.005, 101.322
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

#1: Protein N-acetyltransferase domain-containing protein


Mass: 26121.057 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 6HIS-KKT23 125-348
Source: (gene. exp.) Trypanosoma brucei brucei TREU927 (eukaryote)
Gene: Tb10.70.0180 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q38AU6
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium tartrate dibasic dehydrate, 0.1 M HEPES pH 7.0, 20% SOKOLAN PA 25 CL

-
Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.63→65.16 Å / Num. obs: 55472 / % possible obs: 96 % / Redundancy: 3.6 % / Biso Wilson estimate: 18.67 Å2 / CC1/2: 1 / Rrim(I) all: 0.083 / Net I/σ(I): 11.5
Reflection shellResolution: 1.63→1.67 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3670 / CC1/2: 0.8 / Rrim(I) all: 0.741 / % possible all: 85.7

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→65.14 Å / SU ML: 0.1784 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 23.4781
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2048 2004 4.99 %
Rwork0.1772 38192 -
obs0.1786 40196 85.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.15 Å2
Refinement stepCycle: LAST / Resolution: 1.75→65.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3465 0 102 421 3988
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00733679
X-RAY DIFFRACTIONf_angle_d1.09844997
X-RAY DIFFRACTIONf_chiral_restr0.059537
X-RAY DIFFRACTIONf_plane_restr0.0055616
X-RAY DIFFRACTIONf_dihedral_angle_d17.27211371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.2996780.26351459X-RAY DIFFRACTION45.83
1.79-1.840.2834990.24981781X-RAY DIFFRACTION56
1.84-1.90.30831060.23292249X-RAY DIFFRACTION70.96
1.9-1.960.22091500.20692798X-RAY DIFFRACTION88.13
1.96-2.030.23011570.19682878X-RAY DIFFRACTION89.85
2.03-2.110.24911520.18712961X-RAY DIFFRACTION93.54
2.11-2.20.22721670.17973008X-RAY DIFFRACTION95.12
2.2-2.320.22221530.17663009X-RAY DIFFRACTION95.15
2.32-2.470.22831570.17913024X-RAY DIFFRACTION95.44
2.47-2.660.20851570.19213040X-RAY DIFFRACTION95.92
2.66-2.920.22691650.1913018X-RAY DIFFRACTION95.36
2.92-3.350.17951520.18033007X-RAY DIFFRACTION94.81
3.35-4.220.16681590.14563020X-RAY DIFFRACTION94.47
4.22-65.140.17151520.15732940X-RAY DIFFRACTION93.05
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)
12.903780385210.0543550588268-0.1103604894220.4289873583240.2586843085030.4124947065050.01481690599520.11143621754-0.303426275348-0.005988715206930.028542975928-0.01138521300020.02472813651990.0126437677033-0.04761872767910.1507918567610.0031207957636-0.02465210626180.0941717382483-0.007632886689450.160438204049-19.2346090963-27.43082219912.6959759879
24.5048570187-0.821871688043-0.3581307592716.295732369352.598648814462.13845403412-0.279720493174-1.203981338260.3563196087661.536767077250.1867185627420.2842849316320.638889967933-0.139032626140.07726737936110.5477054159860.02538762234420.01516604337610.5834047775230.03846402817930.346568811654-17.3819124096-27.082385157232.9434871766
32.06996153970.1539161778540.4698761628810.8936162378310.01824754800771.44690036771-0.0138457359561-0.2394600345590.1466722985370.0814332480392-0.00605145312993-0.0196596477438-0.0724177765386-0.0137058513140.03101038888070.1142337487410.017111310244-0.01196336933070.116105087969-0.02097386036580.108881088606-20.2200598348-15.38743306721.3919319545
42.19658485042-0.484581974261-0.5727664378750.572486833848-0.489099698970.8283543255860.0193527188086-0.1863907464740.0544679346616-0.0213101783630.00394522724832-0.0155354482184-0.00936238890786-0.0311565798636-0.03993637621480.19578237501-0.017829370277-0.007426180725780.1230834580010.02124279337980.174897851294-18.03332733392.309860604085.18888722188
52.48206079044-0.0460982691927-0.710347993321.167517399870.3003380240640.67846676344-0.1218791976260.100786641781-0.291978221257-0.02886719226930.0390675202638-0.01574822720340.0692668842841-0.009661569365830.06096938553870.1301715325810.0043616883253-0.0008752597780880.0956277719150.001328893060380.136610739371-11.4755186187-6.11799240587-2.79844493444
61.592476817210.1600103801740.3499599919980.9689488015710.3586303632410.948206188416-0.004476573651190.325163760103-0.0294308903441-0.189192342890.04831054066170.05924542684540.0552355575279-0.175434679168-0.005387584218020.132655895349-0.012308504226-0.007094826867320.1605172338910.01072720470240.0931669583099-12.65287145643.88617169438-10.969699477
73.58809664101-0.175516345720.1336329611732.023987253810.5729322933782.1769594276-0.0329077411040.3981937286630.445367247872-0.1390122127720.03419057461360.348336604573-0.0526468221737-0.154503757870.05945881920110.170625284225-0.0168149248135-0.01470460154770.1256760891040.02445138153620.153862804076-17.097969535714.5994541398-6.82027785598
82.243511809980.2571578495240.6889416195095.999712126240.6263523707131.72877659033-0.1163379564780.4903404261590.235666124386-0.2075750746480.1400942146880.102301918564-0.103350816831-0.395683224209-0.06735950260930.32093758602-0.0900737907096-0.09011896881870.4511466554930.08151424893530.293636422899-28.89950476118.87315606043-19.579101566
93.29326183625-0.07501461950190.8199514992530.726922903703-0.4407681520510.77285622771-0.105112299720.3642928658960.206711279167-0.1032060854560.0184379861778-0.143049416328-0.04333348127580.1497964199220.06575950757410.205683513083-0.03834572397460.007922657308290.202234244963-0.007588432783930.147777123364-7.834863579047.27197142693-10.5575092825
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 127 through 186 )BA127 - 1861 - 57
22chain 'B' and (resid 187 through 202 )BA187 - 20258 - 69
33chain 'B' and (resid 203 through 347 )BA203 - 34770 - 214
44chain 'A' and (resid 126 through 145 )AC126 - 1451 - 20
55chain 'A' and (resid 146 through 215 )AC146 - 21521 - 81
66chain 'A' and (resid 216 through 275 )AC216 - 27582 - 142
77chain 'A' and (resid 276 through 291 )AC276 - 291143 - 159
88chain 'A' and (resid 292 through 305 )AC292 - 305160 - 173
99chain 'A' and (resid 306 through 348 )AC306 - 348174 - 216

+
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