[English] 日本語
Yorodumi
- PDB-6rxp: Crystal structure of CobB Ac2 (A76G,I131C,V162A) in complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rxp
TitleCrystal structure of CobB Ac2 (A76G,I131C,V162A) in complex with H4K16-Crotonyl peptide
Components
  • Histone H4
  • NAD-dependent protein deacylase
KeywordsHYDROLASE / deacylase / NAD-dependent / Crotonyl
Function / homology
Function and homology information


lipoamidase activity / NAD-dependent protein de-2-hydroxyisobutyrylase activity / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / HATs acetylate histones / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication ...lipoamidase activity / NAD-dependent protein de-2-hydroxyisobutyrylase activity / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / HATs acetylate histones / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / HDACs deacetylate histones / cyclic-di-GMP binding / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / histone deacetylase activity, NAD-dependent / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Oxidative Stress Induced Senescence / RMTs methylate histone arginines / SUMOylation of chromatin organization proteins / RNA Polymerase I Promoter Escape / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / NAD+ poly-ADP-ribosyltransferase activity / NAD+ binding / chemotaxis / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / defense response to virus / protein heterodimerization activity / regulation of DNA-templated transcription / protein homodimerization activity / DNA binding / zinc ion binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Sirtuin, class III / SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain ...Sirtuin, class III / SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone-fold / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone H4 / NAD-dependent protein deacylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSpinck, M. / Gasper, R. / Neumann, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationNE1589/5-1 Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: Evolved, Selective Erasers of Distinct Lysine Acylations.
Authors: Spinck, M. / Neumann-Staubitz, P. / Ecke, M. / Gasper, R. / Neumann, H.
History
DepositionJun 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NAD-dependent protein deacylase
B: NAD-dependent protein deacylase
C: Histone H4
D: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9136
Polymers58,7834
Non-polymers1312
Water6,035335
1
A: NAD-dependent protein deacylase
C: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4573
Polymers29,3912
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-6 kcal/mol
Surface area11760 Å2
MethodPISA
2
B: NAD-dependent protein deacylase
D: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4573
Polymers29,3912
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-7 kcal/mol
Surface area11800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.560, 91.890, 95.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
12chain C
22chain D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSGLYGLYchain AAA40 - 27215 - 247
21LYSLYSLYSLYSchain BBB40 - 27415 - 249
12GLYGLYLEULEUchain CCC13 - 222 - 11
22LYSLYSLEULEUchain DDD12 - 221 - 11

NCS ensembles :
ID
1
2

-
Components

#1: Protein NAD-dependent protein deacylase / Regulatory protein SIR2 homolog


Mass: 28054.656 Da / Num. of mol.: 2 / Fragment: H4K16Cr / Mutation: A76G,I131C,V162A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: cobB, ycfY, b1120, JW1106 / Plasmid: pBAD / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P75960, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein/peptide Histone H4


Mass: 1336.653 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P02309
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.16 Å3/Da / Density % sol: 42.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M Bis-Tris, 0.03 M HCl, 23% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→47.95 Å / Num. obs: 47854 / % possible obs: 100 % / Redundancy: 12.616 % / Biso Wilson estimate: 30.68 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.088 / Χ2: 1.008 / Net I/σ(I): 15.26 / Num. measured all: 603730 / Scaling rejects: 74
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.8512.4391.4211.9743299348434810.8351.48299.9
1.85-1.911.7771.1192.5340019339933980.8981.17100
1.9-1.9513.0730.7873.7743273331133100.9370.819100
1.95-2.0113.4560.5814.9443423322732270.9620.604100
2.01-2.0813.3170.4616.0441484311531150.9780.48100
2.08-2.1513.2940.3647.6340161302130210.9830.379100
2.15-2.2313.1720.2799.7238686293729370.9890.29100
2.23-2.3212.6120.24611.135490281428140.990.257100
2.32-2.4311.7980.1912.8131761269326920.9950.199100
2.43-2.5513.230.14816.234465260526050.9970.155100
2.55-2.6813.3720.11919.732961246524650.9970.124100
2.68-2.8513.0110.10522.2130484234423430.9970.11100
2.85-3.0412.5950.0925.8527823220922090.9970.094100
3.04-3.2911.6260.08127.2924124207620750.9980.085100
3.29-3.610.7450.06729.7420490190819070.9980.0799.9
3.6-4.0212.2890.0635.7621346173717370.9980.062100
4.02-4.6512.5090.05438.6719151153215310.9990.05699.9
4.65-5.6911.9940.05238.3915856132213220.9990.054100
5.69-8.0511.2520.04737.4511837105210520.9990.049100
8.05-47.9512.3930.04441.2675976176130.9990.04699.4

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.88 Å47.95 Å
Translation6.88 Å47.95 Å

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSVERSION JAN 31, 2018data reduction
XSCALEVERSION JAN 31, 2018data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 1S5P

1s5p


Resolution: 1.8→47.95 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2336 2005 4.19 %
Rwork0.1924 45835 -
obs0.1942 47840 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.21 Å2 / Biso mean: 39.2335 Å2 / Biso min: 20.99 Å2
Refinement stepCycle: final / Resolution: 1.8→47.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3815 0 2 335 4152
Biso mean--42.08 43.85 -
Num. residues----489
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073922
X-RAY DIFFRACTIONf_angle_d1.1165314
X-RAY DIFFRACTIONf_chiral_restr0.05568
X-RAY DIFFRACTIONf_plane_restr0.006707
X-RAY DIFFRACTIONf_dihedral_angle_d14.481450
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2024X-RAY DIFFRACTION10.206TORSIONAL
12B2024X-RAY DIFFRACTION10.206TORSIONAL
21C58X-RAY DIFFRACTION10.206TORSIONAL
22D58X-RAY DIFFRACTION10.206TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8001-1.84510.32061440.28532103354
1.8451-1.8950.28411250.254332203345
1.895-1.95070.30371600.238632153375
1.9507-2.01370.26861400.22232493389
2.0137-2.08570.29581390.220432443383
2.0857-2.16920.24821380.20332403378
2.1692-2.26790.24821460.19432393385
2.2679-2.38750.26961420.204632573399
2.3875-2.5370.20861400.197232783418
2.537-2.73290.2341470.196432653412
2.7329-3.00790.26161410.210232833424
3.0079-3.4430.26991510.200432983449
3.443-4.33740.18451440.167133433487
4.3374-47.9670.2091480.174734943642

+
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