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- PDB-7aqm: ADP-ribosylserine hydrolase ARH3 of Latimeria chalumnae in comple... -

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Basic information

Entry
Database: PDB / ID: 7aqm
TitleADP-ribosylserine hydrolase ARH3 of Latimeria chalumnae in complex with alpha-1''-O-methyl-ADP-ribose (meADPr)
ComponentsADP-ribosylhydrolase like 2
KeywordsHYDROLASE / ADP-ribosylserine hydrolase / ARH3 / Latimeria chalumnae / alpha-1''-O-methyl-ADP ribose
Function / homology
Function and homology information


peptidyl-serine ADP-deribosylation / poly(ADP-ribose) glycohydrolase / poly(ADP-ribose) glycohydrolase activity / negative regulation of necroptotic process / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / chromosome / mitochondrial matrix / DNA repair / magnesium ion binding / nucleus
Similarity search - Function
ADP-ribosylation/Crystallin J1 / ADP-ribosylglycohydrolase / ADP-ribosylation/Crystallin J1 superfamily
Similarity search - Domain/homology
Chem-RVK / ADP-ribosylhydrolase ARH3
Similarity search - Component
Biological speciesLatimeria chalumnae (coelacanth)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRack, J.G.M. / Zorzini, V. / Ahel, I.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust101794 United Kingdom
Wellcome Trust210634 United Kingdom
CitationJournal: Nat Commun / Year: 2021
Title: Mechanistic insights into the three steps of poly(ADP-ribosylation) reversal.
Authors: Rack, J.G.M. / Liu, Q. / Zorzini, V. / Voorneveld, J. / Ariza, A. / Honarmand Ebrahimi, K. / Reber, J.M. / Krassnig, S.C. / Ahel, D. / van der Marel, G.A. / Mangerich, A. / McCullagh, J.S.O. ...Authors: Rack, J.G.M. / Liu, Q. / Zorzini, V. / Voorneveld, J. / Ariza, A. / Honarmand Ebrahimi, K. / Reber, J.M. / Krassnig, S.C. / Ahel, D. / van der Marel, G.A. / Mangerich, A. / McCullagh, J.S.O. / Filippov, D.V. / Ahel, I.
History
DepositionOct 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / database_PDB_rev / database_PDB_rev_record / diffrn_source / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id ..._diffrn_source.pdbx_synchrotron_site / _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: ADP-ribosylhydrolase like 2
B: ADP-ribosylhydrolase like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8238
Polymers76,5792
Non-polymers1,2446
Water95553
1
A: ADP-ribosylhydrolase like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9114
Polymers38,2901
Non-polymers6223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA and gel filtration
2
B: ADP-ribosylhydrolase like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9114
Polymers38,2901
Non-polymers6223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA and gel filtration
Unit cell
Length a, b, c (Å)66.825, 97.613, 107.396
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
11(chain A and (resid 8 through 34 or (resid 35...
21(chain B and (resid 8 through 53 or (resid 54...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROGLYGLY(chain A and (resid 8 through 34 or (resid 35...AA8 - 342 - 28
12SERSERALAALA(chain A and (resid 8 through 34 or (resid 35...AA35 - 3729 - 31
13PROPROLEULEU(chain A and (resid 8 through 34 or (resid 35...AA8 - 3532 - 347
14PROPROLEULEU(chain A and (resid 8 through 34 or (resid 35...AA8 - 3532 - 347
15PROPROLEULEU(chain A and (resid 8 through 34 or (resid 35...AA8 - 3532 - 347
16PROPROLEULEU(chain A and (resid 8 through 34 or (resid 35...AA8 - 3532 - 347
21PROPROGLUGLU(chain B and (resid 8 through 53 or (resid 54...BB8 - 532 - 47
22LYSLYSALAALA(chain B and (resid 8 through 53 or (resid 54...BB54 - 5648 - 50
23PROPROLEULEU(chain B and (resid 8 through 53 or (resid 54...BB8 - 3532 - 347
24PROPROLEULEU(chain B and (resid 8 through 53 or (resid 54...BB8 - 3532 - 347
25PROPROLEULEU(chain B and (resid 8 through 53 or (resid 54...BB8 - 3532 - 347
26PROPROLEULEU(chain B and (resid 8 through 53 or (resid 54...BB8 - 3532 - 347

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Components

#1: Protein ADP-ribosylhydrolase like 2


Mass: 38289.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Latimeria chalumnae (coelacanth) / Gene: ADPRHL2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: H3BCW1, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides, poly(ADP-ribose) glycohydrolase, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-RVK / Adenosine 5'-diphosphoric acid beta-[(3beta,4beta-dihydroxy-5beta-methoxytetrahydrofuran-2alpha-yl)methyl] estere / [[(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~{S},4~{R},5~{S})-5-methoxy-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate / [[(2R,3S,4R,5R)-5-(6-Aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy-hydroxyphosphoryl] [(2R,3S,4R,5S)-3,4-dihydroxy-5-methoxyoxolan-2-yl]methyl hydrogen phosphate / J3.653.949F / alpha-1''-O-methyl-ADP ribose


Mass: 573.342 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H25N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 100 mM Na-citrate (pH 5) 200 mM ammonium acetate 22% (w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.34→56.72 Å / Num. obs: 30398 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 54.17 Å2 / Rpim(I) all: 0.081 / Rrim(I) all: 0.293 / Net I/σ(I): 5.6 / Num. measured all: 393655
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2% possible allRpim(I) allRrim(I) all
2.34-2.3811.90.214960.21399.1
6.35-56.7412.133.216731000.0180.063

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HH3

6hh3


Resolution: 2.5→53.698 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 36.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2834 1971 7.98 %
Rwork0.2231 22724 -
obs0.2281 24695 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.66 Å2 / Biso mean: 74.4978 Å2 / Biso min: 30.66 Å2
Refinement stepCycle: final / Resolution: 2.5→53.698 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4900 0 78 53 5031
Biso mean--82.09 61.16 -
Num. residues----657
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2872X-RAY DIFFRACTION5.12TORSIONAL
12B2872X-RAY DIFFRACTION5.12TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.56250.40111370.3863156998
2.5625-2.63180.40981380.3505159499
2.6318-2.70930.41781350.334156498
2.7093-2.79670.35361380.3101158398
2.7967-2.89670.34471410.2889161599
2.8967-3.01260.34931400.2755160599
3.0126-3.14970.38581390.2676159199
3.1497-3.31580.34151370.2409162499
3.3158-3.52350.27221410.2231163199
3.5235-3.79540.25731400.2069161899
3.7954-4.17730.23121430.1822164099
4.1773-4.78140.25321420.174164899
4.7814-6.02280.26581480.21591682100
6.0228-53.6980.24211520.1879176099
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9674-1.5960.88174.29151.52626.0030.2476-0.2552-0.20560.227-0.4111-0.05280.29980.05940.12570.28260.0590.02550.63490.26170.399912.962719.139115.5148
26.9925-1.83480.76037.3867-1.74176.38210.12392.037-0.4072-0.42310.01671.41510.0101-1.05-0.22110.4216-0.2002-0.12611.09870.04880.8985-3.666514.41388.1852
36.7365-1.3060.31993.0653-0.01912.26520.1654-0.316-1.4324-0.03680.09730.31630.19530.1346-0.24540.3655-0.0321-0.05940.65470.0840.657216.48164.041622.4943
44.50980.10664.04481.4604-1.16284.72090.5724-0.0332-1.66270.34720.4017-0.2460.46420.4881-0.51680.63340.2649-0.161.306-0.14491.665724.8171-7.559813.8178
57.0152-0.39721.08443.4923-0.02381.66630.23981.6132-0.6343-0.2244-0.1172-0.53330.12680.3508-0.11810.40850.0451-0.00971.38780.09020.639625.9819.87810.4125
63.23484.0299-1.16575.0173-1.31432.28870.32131.74480.7626-0.82560.3737-0.4559-0.24991.1218-0.910.68340.07160.152.07980.21280.690225.991319.6801-0.6818
72.251-0.72730.62672.8628-0.46331.94010.36321.4831-0.0917-0.4481-0.21250.2596-0.0830.1992-0.20910.45090.10510.0021.18330.10130.513112.116617.22896.1864
82-2.861222220.72954.6497-4.1652-9.4605-4.31563.19778.293-11.21583.57691.1292-0.1705-0.11750.9656-0.03620.618237.806124.240222.1767
98.78235.9994-5.61977.4967-5.19096.6155-0.1807-1.11670.1676-0.6509-0.2594-0.35920.24960.1620.41960.35310.0888-0.00760.3859-0.12240.5071-6.9193-18.45815.6252
102.7631-0.60980.36513.53941.20233.65320.09120.1592-0.1375-0.5257-0.325-0.4429-0.43750.9811-0.21410.47540.0677-0.01790.5297-0.08990.54351.0601-11.733815.658
113.434-0.68470.63042.2707-0.6471.23010.05410.36750.0939-0.0585-0.08650.3953-0.0566-0.44450.02580.45020.03950.00110.7958-0.03310.6747-17.7472-1.824614.3249
124.50180.24420.03414.2897-0.01642.34670.15030.9422-0.4643-0.7396-0.16140.00730.1081-0.46510.00970.66060.108-0.01611.2111-0.17070.6436-12.1548-14.614-3.5718
133.4152-0.2133-0.69021.2173-1.21792.6643-0.19440.2485-0.1653-0.11050.1692-0.2790.15140.19070.17160.48810.008-0.03040.6673-0.21380.5433-5.1768-19.836213.0155
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 32 )A8 - 32
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 52 )A33 - 52
3X-RAY DIFFRACTION3chain 'A' and (resid 53 through 114 )A53 - 114
4X-RAY DIFFRACTION4chain 'A' and (resid 115 through 137 )A115 - 137
5X-RAY DIFFRACTION5chain 'A' and (resid 138 through 188 )A138 - 188
6X-RAY DIFFRACTION6chain 'A' and (resid 189 through 208 )A189 - 208
7X-RAY DIFFRACTION7chain 'A' and (resid 209 through 353 )A209 - 353
8X-RAY DIFFRACTION8chain 'A' and (resid 403 through 403 )A403
9X-RAY DIFFRACTION9chain 'B' and (resid 8 through 32 )B8 - 32
10X-RAY DIFFRACTION10chain 'B' and (resid 33 through 77 )B33 - 77
11X-RAY DIFFRACTION11chain 'B' and (resid 78 through 188 )B78 - 188
12X-RAY DIFFRACTION12chain 'B' and (resid 189 through 277 )B189 - 277
13X-RAY DIFFRACTION13chain 'B' and (resid 278 through 353 )B278 - 353

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