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

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Basic information

Entry
Database: PDB / ID: 6hoz
TitleADP-ribosylserine hydrolase ARH3 of Latimeria chalumnae in complex with inosine diphosphate ribose (IDPr)
ComponentsADP-ribosylhydrolase like 2
KeywordsHYDROLASE / ADP-ribosylation / ADP-ribose / ADPRHL2 / ADP-ribosylhydrolase like 2 / inosine diphosphate ribose / IDPr
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-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
ACETATE ION / inosine diphosphate ribose / inosine diphosphate ribose / ADP-ribosylhydrolase ARH3
Similarity search - Component
Biological speciesLatimeria chalumnae (coelacanth)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 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
DepositionSep 18, 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 2.0Jan 2, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.label_alt_id / _atom_site_anisotrop.pdbx_label_alt_id / _citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_validate_close_contact.label_alt_id_2
Revision 2.1Jan 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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)79,89721
Polymers76,5792
Non-polymers3,31819
Water7,512417
1
A: ADP-ribosylhydrolase like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,97811
Polymers38,2901
Non-polymers1,68910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ADP-ribosylhydrolase like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,91910
Polymers38,2901
Non-polymers1,6309
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.844, 96.933, 107.519
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: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 9 - 353 / Label seq-ID: 3 - 347

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

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 6 types, 436 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-R5I / inosine diphosphate ribose


Mass: 560.301 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N4O15P2
#4: Chemical ChemComp-R7I / inosine diphosphate ribose


Mass: 560.301 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N4O15P2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 2.42 Å3/Da / Density % sol: 49.21 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
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: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.77→96.95 Å / Num. obs: 68856 / % possible obs: 100 % / Redundancy: 12.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.051 / Rrim(I) all: 0.13 / Χ2: 0.96 / Net I/σ(I): 10.9
Reflection shellResolution: 1.77→1.82 Å / Redundancy: 10.2 % / Rmerge(I) obs: 1.896 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 5010 / CC1/2: 0.745 / Rpim(I) all: 0.912 / Rrim(I) all: 2.108 / Χ2: 0.98 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FOZ

2foz


Resolution: 1.77→72.1 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / SU B: 5.435 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18872 3396 4.9 %RANDOM
Rwork0.15812 ---
obs0.15963 65347 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.833 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å20 Å2
2---0.12 Å20 Å2
3---1.32 Å2
Refinement stepCycle: 1 / Resolution: 1.77→72.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5043 0 212 417 5672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0145526
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175035
X-RAY DIFFRACTIONr_angle_refined_deg1.5121.6677466
X-RAY DIFFRACTIONr_angle_other_deg1.0411.65511823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4465695
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.30723.077260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.40115946
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1681528
X-RAY DIFFRACTIONr_chiral_restr0.0810.2744
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026067
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02977
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_it1.211.8452666
X-RAY DIFFRACTIONr_mcbond_other1.2061.8442665
X-RAY DIFFRACTIONr_mcangle_it1.9482.7573337
X-RAY DIFFRACTIONr_mcangle_other1.9482.7583338
X-RAY DIFFRACTIONr_scbond_it1.6982.1032860
X-RAY DIFFRACTIONr_scbond_other1.6982.1032860
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6113.0444108
X-RAY DIFFRACTIONr_long_range_B_refined5.47123.0446373
X-RAY DIFFRACTIONr_long_range_B_other5.3622.5546297
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 10947 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 247 -
Rwork0.291 4760 -
obs--99.86 %
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)
12.65760.4386-0.27691.273-0.02030.95230.0629-0.03780.26390.06590.00610.02350.04330.0458-0.06890.01930.01470.01080.0429-0.00310.060216.135-11.515-10.702
21.60250.24860.12831.5815-0.12571.0020.0159-0.0740.01640.10250.0241-0.0026-0.0432-0.0319-0.040.01720.01030.00250.0707-0.00560.0195-10.08911.123-10.313
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 701
2X-RAY DIFFRACTION2B9 - 605

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