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- PDB-6rxp: Crystal structure of CobB Ac2 (A76G,I131C,V162A) in complex with ... -

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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 / HDMs demethylate histones / HATs acetylate histones / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / Condensation of Prophase Chromosomes / RNA polymerase I upstream activating factor complex / SUMOylation of chromatin organization proteins / NAD-dependent protein lysine deacetylase activity ...lipoamidase activity / NAD-dependent protein de-2-hydroxyisobutyrylase activity / HDMs demethylate histones / HATs acetylate histones / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / Condensation of Prophase Chromosomes / RNA polymerase I upstream activating factor complex / SUMOylation of chromatin organization proteins / NAD-dependent protein lysine deacetylase activity / cyclic-di-GMP binding / protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / replication fork protection complex / RMTs methylate histone arginines / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / NAD+ ADP-ribosyltransferase activity / NAD+ binding / nucleosome assembly / structural constituent of chromatin / chemotaxis / nucleosome / chromatin organization / defense response to virus / protein heterodimerization activity / regulation of DNA-templated transcription / protein homodimerization activity / DNA binding / zinc ion 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 / DHS-like NAD/FAD-binding domain superfamily ...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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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 / Water


Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

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

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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

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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

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Phasing

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

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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

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