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- PDB-6rxr: Crystal structure of CobB Ac2 (A76G, I131C, V162G) in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6rxr
TitleCrystal structure of CobB Ac2 (A76G, I131C, V162G) in complex with H4K16Cr-2'OH-ADPr peptide intermediate after co-crystallisation
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 / 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
Chem-KMQ / 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 / Resolution: 1.7 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_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: NAD-dependent protein deacylase
D: NAD-dependent protein deacylase
E: Histone H4
F: Histone H4
G: Histone H4
H: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,75112
Polymers117,2978
Non-polymers2,4544
Water10,485582
1
A: NAD-dependent protein deacylase
E: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9383
Polymers29,3242
Non-polymers6131
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-10 kcal/mol
Surface area11210 Å2
MethodPISA
2
B: NAD-dependent protein deacylase
F: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9383
Polymers29,3242
Non-polymers6131
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-9 kcal/mol
Surface area11430 Å2
MethodPISA
3
C: NAD-dependent protein deacylase
G: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9383
Polymers29,3242
Non-polymers6131
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-10 kcal/mol
Surface area11140 Å2
MethodPISA
4
D: NAD-dependent protein deacylase
H: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9383
Polymers29,3242
Non-polymers6131
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-10 kcal/mol
Surface area11320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.380, 94.070, 94.060
Angle α, β, γ (deg.)90.000, 90.030, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
12chain E
22chain F
32chain G

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA40 - 274
211chain BB39 - 274
311chain CC40 - 274
411chain DD40 - 274
112chain EE13 - 21
212chain FF13 - 22
312chain GG13 - 21

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.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: cobB, ycfY, b1120, JW1106 / 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: 1269.586 Da / Num. of mol.: 4 / Source method: obtained synthetically
Source: (synth.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P02309
#3: Chemical
ChemComp-KMQ / [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{S})-4-[(~{E})-but-2-enoxy]-3,5-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate


Mass: 613.406 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H29N5O14P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 582 / 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: 2.38 Å3/Da / Density % sol: 43.96 % / Description: 48.4
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 0.1 M Bis-Tris, 0.02 M HCl, 22% PEG 3350, 1 mM NAD

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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: 1.7→45.115 Å / Num. obs: 117240 / % possible obs: 100 % / Redundancy: 6.723 % / Biso Wilson estimate: 32.79 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.047 / Rrim(I) all: 0.051 / Χ2: 1.031 / Net I/σ(I): 20.1 / Num. measured all: 788173 / Scaling rejects: 27
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
1.7-1.746.8841.4961.2559182860485970.6391.61999.9
1.74-1.796.7811.0871.7556948840083980.7821.178100
1.79-1.846.6140.7892.4954678827182670.8440.857100
1.84-1.96.1920.5083.8749166794579400.930.55699.9
1.9-1.966.8130.4145.2452362768976860.950.449100
1.96-2.036.9330.3216.9951854748074790.9720.347100
2.03-2.116.8450.2359.4749276720571990.9810.25599.9
2.11-2.196.8920.20212.4547974696569610.9860.21899.9
2.19-2.296.8230.15815.9345843672067190.990.172100
2.29-2.46.3490.12119.1239934629262900.9950.132100
2.4-2.536.8460.08924.7741681608860880.9970.097100
2.53-2.697.0890.07130.4940598572757270.9980.076100
2.69-2.876.9890.05835.3437722539853970.9980.063100
2.87-3.16.7750.04641.1233956501250120.9990.05100
3.1-3.46.1720.03745.2128618463946370.9990.041100
3.4-3.86.4550.02953.4327042419141890.9990.032100
3.8-4.396.910.02560.0525691371937180.9990.027100
4.39-5.386.7240.02361.89210863136313610.025100
5.38-7.66.1190.02557.4114919244124380.9990.02799.9
7.6-45.1157.080.02367.669643137013620.9990.02599.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSVERSION JAN 31, 2018data reduction
XSCALEVERSION JAN 31, 2018data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.5data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 1S5P

1s5p


Resolution: 1.7→45.115 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2283 1989 1.7 %
Rwork0.1989 115191 -
obs0.1994 117180 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.25 Å2 / Biso mean: 44.7376 Å2 / Biso min: 21.09 Å2
Refinement stepCycle: final / Resolution: 1.7→45.115 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7460 0 0 586 8046
Biso mean---48.29 -
Num. residues----937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057943
X-RAY DIFFRACTIONf_angle_d1.28410815
X-RAY DIFFRACTIONf_chiral_restr0.0491168
X-RAY DIFFRACTIONf_plane_restr0.0051378
X-RAY DIFFRACTIONf_dihedral_angle_d17.1333008
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4244X-RAY DIFFRACTION6.102TORSIONAL
12B4244X-RAY DIFFRACTION6.102TORSIONAL
13C4244X-RAY DIFFRACTION6.102TORSIONAL
14D4244X-RAY DIFFRACTION6.102TORSIONAL
21E74X-RAY DIFFRACTION6.102TORSIONAL
22F74X-RAY DIFFRACTION6.102TORSIONAL
23G74X-RAY DIFFRACTION6.102TORSIONAL
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
1.7-1.74250.32281410.319181178258
1.7425-1.78960.31581370.313782048341
1.7896-1.84230.35041420.304982538395
1.8423-1.90170.33061370.271381908327
1.9017-1.96970.34921430.264282228365
1.9697-2.04860.21591430.24182058348
2.0486-2.14180.22051390.23781698308
2.1418-2.25470.28341440.216682548398
2.2547-2.3960.2461370.216181878324
2.396-2.5810.27021410.210982248365
2.581-2.84070.30151540.208382598413
2.8407-3.25160.23991400.212782908430
3.2516-4.09630.19351410.177382508391
4.0963-45.1310.17651500.155283678517

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