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- PDB-6rxj: Crystal structure of CobB wt in complex with H4K16-Acetyl peptide -

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Basic information

Entry
Database: PDB / ID: 6rxj
TitleCrystal structure of CobB wt in complex with H4K16-Acetyl peptide
Components
  • Histone H4
  • NAD-dependent protein deacylase
KeywordsHYDROLASE / deacylase / NAD-dependent / Acetyl / Lysine / PTM
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 / NAD-dependent protein lysine deacetylase activity / cyclic-di-GMP binding / 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: 1.6 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 1.2Sep 27, 2023Group: 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 / 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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 2.1Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)58,7396
Polymers58,6084
Non-polymers1312
Water5,224290
1
A: NAD-dependent protein deacylase
C: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3703
Polymers29,3042
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-8 kcal/mol
Surface area11590 Å2
MethodPISA
2
B: NAD-dependent protein deacylase
D: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3703
Polymers29,3042
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-8 kcal/mol
Surface area11710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.100, 131.260, 58.540
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-503-

HOH

21B-508-

HOH

31B-529-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 40 - 274 / Label seq-ID: 15 - 249

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

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


Mass: 28106.750 Da / Num. of mol.: 2 / Fragment: H4K16Ac
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: 1197.457 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: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.14 Å3/Da / Density % sol: 42.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M Bis-Tris, 0.03 M HCl, 22% 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: 1.6→46.379 Å / Num. obs: 66812 / % possible obs: 99.9 % / Redundancy: 13.001 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.07 / Χ2: 1.02 / Net I/σ(I): 18.83 / Num. measured all: 868617 / Scaling rejects: 22
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
1.6-1.6413.171.6181.663756486448410.6441.68299.5
1.64-1.6912.5271.4271.8160027480547920.6841.48899.7
1.69-1.7412.5541.1032.4957774461246020.7761.14999.8
1.74-1.7913.70.8323.5661772451545090.8980.86499.9
1.79-1.8513.4760.5945.0758892437543700.9490.61799.9
1.85-1.9113.4640.4297.1656913422842270.9760.445100
1.91-1.9813.3860.319.6654962410841060.9870.322100
1.98-2.0713.2280.22812.7552053393539350.9920.238100
2.07-2.1612.360.18514.9347117381238120.9930.193100
2.16-2.2613.5630.13919.9649137362436230.9960.144100
2.26-2.3913.9860.11523.2448126344134410.9980.119100
2.39-2.5313.6850.09427.6244724326832680.9980.098100
2.53-2.713.410.07831.9641181307130710.9980.081100
2.7-2.9212.4740.06835.9636126289628960.9980.071100
2.92-3.211.4590.05440.230457265826580.9990.056100
3.2-3.5812.940.04549.9731121240524050.9990.047100
3.58-4.1312.5190.03954.7326853214521450.9990.041100
4.13-5.0611.9080.03755.8221685182118210.9990.039100
5.06-7.1610.9190.03951.9515844145414510.9990.0499.8
7.16-46.37912.0350.03357.82100978438390.9990.03599.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.49 Å49.5 Å
Translation5.49 Å49.5 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: 1S5P

1s5p


Resolution: 1.6→46.379 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1876 2013 3.01 %
Rwork0.1731 64788 -
obs0.1736 66801 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.93 Å2 / Biso mean: 39.1659 Å2 / Biso min: 17.74 Å2
Refinement stepCycle: final / Resolution: 1.6→46.379 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3795 0 2 290 4087
Biso mean--30.29 41.39 -
Num. residues----485
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083891
X-RAY DIFFRACTIONf_angle_d1.1115274
X-RAY DIFFRACTIONf_chiral_restr0.043566
X-RAY DIFFRACTIONf_plane_restr0.005704
X-RAY DIFFRACTIONf_dihedral_angle_d15.2441435
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2774X-RAY DIFFRACTION6.78TORSIONAL
12B2774X-RAY DIFFRACTION6.78TORSIONAL
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
1.6001-1.64010.30911410.299145384679
1.6401-1.68440.29851400.282745734713
1.6844-1.7340.22571420.252645724714
1.734-1.790.24541420.231745864728
1.79-1.85390.27041430.210445834726
1.8539-1.92820.21851440.18845814725
1.9282-2.01590.2111420.1846354777
2.0159-2.12220.17061400.174645774717
2.1222-2.25520.20071420.168146424784
2.2552-2.42930.19381440.167146334777
2.4293-2.67370.18331430.165546554798
2.6737-3.06060.22881480.176646434791
3.0606-3.85570.20331410.164847144855
3.8557-46.39860.14121610.157348565017

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