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- PDB-6g1q: ADP-ribosylserine hydrolase ARH3 of Latimeria chalumnae in comple... -

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Basic information

Entry
Database: PDB / ID: 6g1q
TitleADP-ribosylserine hydrolase ARH3 of Latimeria chalumnae in complex with ADP-ribose
ComponentsADP-ribosylhydrolase like 2
KeywordsHYDROLASE / ADP-ribosylation / ADP-ribose / ADPRHL2 / ADP-ribosylhydrolase like 2
Function / homology
Function and homology information


peptidyl-serine ADP-deribosylation / ADP-ribosylserine hydrolase activity / poly(ADP-ribose) glycohydrolase activity / poly(ADP-ribose) glycohydrolase / 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 ...peptidyl-serine ADP-deribosylation / ADP-ribosylserine hydrolase activity / poly(ADP-ribose) glycohydrolase activity / poly(ADP-ribose) glycohydrolase / 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-ribosylglycohydrolase fold / ADP-ribosylation/Crystallin J1 / ADP-ribosylation/Crystallin J1 / ADP-ribosylglycohydrolase / ADP-ribosylation/Crystallin J1 superfamily / : / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-AR6 / ADP-ribosylhydrolase ARH3
Similarity search - Component
Biological speciesLatimeria chalumnae (coelacanth)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAriza, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust101794 United Kingdom
CitationJournal: Cell Chem Biol / Year: 2018
Title: (ADP-ribosyl)hydrolases: Structural Basis for Differential Substrate Recognition and Inhibition.
Authors: Rack, J.G.M. / Ariza, A. / Drown, B.S. / Henfrey, C. / Bartlett, E. / Shirai, T. / Hergenrother, P.J. / Ahel, I.
History
DepositionMar 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_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)77,7466
Polymers76,5792
Non-polymers1,1674
Water1,26170
1
A: ADP-ribosylhydrolase like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8733
Polymers38,2901
Non-polymers5842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ADP-ribosylhydrolase like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8733
Polymers38,2901
Non-polymers5842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.905, 97.458, 105.503
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 7 - 353 / Label seq-ID: 1 - 347

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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 (E. coli) / References: UniProt: H3BCW1
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

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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: 2.26 Å3/Da / Density % sol: 45.61 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 200 mM ammonium acetate, 21 % PEG4000, 100 mM citrate pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→55.16 Å / Num. obs: 41057 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.035 / Rrim(I) all: 0.092 / Net I/σ(I): 13.8
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.903 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3339 / CC1/2: 0.836 / Rpim(I) all: 0.364 / Rrim(I) all: 0.974 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FOZ

2foz


Resolution: 2.1→55.16 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 24.662 / SU ML: 0.246 / Cross valid method: THROUGHOUT / ESU R: 0.252 / ESU R Free: 0.203 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25839 2002 4.9 %RANDOM
Rwork0.21751 ---
obs0.21953 38994 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 61.126 Å2
Baniso -1Baniso -2Baniso -3
1--2.85 Å2-0 Å2-0 Å2
2---1.19 Å20 Å2
3---4.04 Å2
Refinement stepCycle: 1 / Resolution: 2.1→55.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5078 0 74 70 5222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0145309
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174843
X-RAY DIFFRACTIONr_angle_refined_deg1.5591.6737176
X-RAY DIFFRACTIONr_angle_other_deg1.0031.64711356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4165672
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.11522.992254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.29515916
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2791528
X-RAY DIFFRACTIONr_chiral_restr0.080.2696
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025928
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02958
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9963.6572661
X-RAY DIFFRACTIONr_mcbond_other1.9963.6562660
X-RAY DIFFRACTIONr_mcangle_it3.1865.4773324
X-RAY DIFFRACTIONr_mcangle_other3.1865.4783325
X-RAY DIFFRACTIONr_scbond_it2.183.8872648
X-RAY DIFFRACTIONr_scbond_other2.183.8872649
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4155.7323847
X-RAY DIFFRACTIONr_long_range_B_refined5.09543.7816191
X-RAY DIFFRACTIONr_long_range_B_other5.09143.7836189
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 11117 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.49 145 -
Rwork0.456 2862 -
obs--100 %
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)
12.08450.1786-0.07532.74680.32310.76250.02590.14380.181-0.2001-0.16320.22520.0026-0.01720.13730.020.0344-0.02710.2522-0.07110.150723.46637.716115.36
23.6105-0.43840.46882.88150.09320.31280.18250.5422-0.3251-0.1483-0.111-0.1867-0.11490.0325-0.07150.08590.0470.00620.36580.08240.162150.01160.364116.23
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 550
2X-RAY DIFFRACTION2B7 - 537

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