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

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Basic information

Entry
Database: PDB / ID: 6rxo
TitleCrystal structure of CobB Ac2 (A76G, I131C, V162A) in complex with H4K16-Buturyl peptide
Components
  • Histone H4
  • NAD-dependent protein deacylase
KeywordsHYDROLASE / deacylase / NAD-dependent
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 / 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. ...Sirtuin, class III / 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 / 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: 1.95 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 / 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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _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)58,9176
Polymers58,7874
Non-polymers1312
Water3,369187
1
A: NAD-dependent protein deacylase
C: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4593
Polymers29,3932
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-6 kcal/mol
Surface area12100 Å2
MethodPISA
2
B: NAD-dependent protein deacylase
D: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4593
Polymers29,3932
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-6 kcal/mol
Surface area11950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.490, 92.440, 94.450
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

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: 28054.656 Da / Num. of mol.: 2 / 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: 1338.668 Da / Num. of mol.: 2 / Fragment: H4K16Ac / Mutation: K16ALY / 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 / Water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.25 Å3/Da / Density % sol: 45.24 %
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: 1.95→47.225 Å / Num. obs: 39331 / % possible obs: 100 % / Redundancy: 13.072 % / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.083 / Χ2: 1.005 / Net I/σ(I): 18.02 / Num. measured all: 514125 / Scaling rejects: 52
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
1.95-213.0551.6991.7237442286828680.7531.768100
2-2.0613.6761.3352.3238292280128000.8161.387100
2.06-2.1213.5831.0083.136648269926980.8861.048100
2.12-2.1813.4540.8083.7835573264426440.9280.84100
2.18-2.2513.1860.5915.0733927257325730.9580.615100
2.25-2.3312.5970.4865.8331404249324930.9670.506100
2.33-2.4212.780.3687.7630787240924090.9820.383100
2.42-2.5213.7410.28710.1731591229922990.9890.298100
2.52-2.6313.6170.21412.9130462223722370.9940.223100
2.63-2.7613.5030.16915.5728708212621260.9960.176100
2.76-2.9113.2350.12719.6226695201820170.9970.133100
2.91-3.0812.1430.09723.9923558194019400.9980.102100
3.08-3.313.4510.07132.4224279180518050.9990.074100
3.3-3.5613.3690.05738.822768170417030.9990.0699.9
3.56-3.912.8790.04945.3120014155415540.9990.051100
3.9-4.3611.770.04448.2816867143314330.9990.046100
4.36-5.0312.2270.03952.4815541127112710.9990.041100
5.03-6.1712.6620.04250.9913865109510950.9990.044100
6.17-8.7211.510.03752.5598648578570.9990.039100
8.72-47.22511.4730.03157.9158405125090.9990.03299.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.95 Å47.22 Å
Translation1.95 Å47.22 Å

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Processing

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

1s5p


Resolution: 1.95→47.225 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.89
RfactorNum. reflection% reflection
Rfree0.2147 1994 5.07 %
Rwork0.1972 --
obs0.1981 39317 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 101.29 Å2 / Biso mean: 47.9014 Å2 / Biso min: 25.63 Å2
Refinement stepCycle: final / Resolution: 1.95→47.225 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3814 0 2 187 4003
Biso mean--59.46 48.02 -
Num. residues----488
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043923
X-RAY DIFFRACTIONf_angle_d0.8825314
X-RAY DIFFRACTIONf_chiral_restr0.037566
X-RAY DIFFRACTIONf_plane_restr0.005711
X-RAY DIFFRACTIONf_dihedral_angle_d15.8881450
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2122X-RAY DIFFRACTION9.14TORSIONAL
12B2122X-RAY DIFFRACTION9.14TORSIONAL
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
1.9499-1.99870.36031430.302526272770
1.9987-2.05270.28231370.285226242761
2.0527-2.11310.30691380.251426272765
2.1131-2.18140.27111440.243826252769
2.1814-2.25930.22281360.222926512787
2.2593-2.34980.23821420.224526152757
2.3498-2.45670.23911410.220926542795
2.4567-2.58620.23911490.206926272776
2.5862-2.74820.2991440.215826712815
2.7482-2.96040.23411420.218726492791
2.9604-3.25830.21941400.214626792819
3.2583-3.72960.19641420.194726972839
3.7296-4.69820.16751450.159727242869
4.6982-47.23880.19751510.175328533004

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