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- PDB-6hh4: ADP-ribosylserine hydrolase ARH3 of Latimeria chalumnae in comple... -

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Basic information

Entry
Database: PDB / ID: 6hh4
TitleADP-ribosylserine hydrolase ARH3 of Latimeria chalumnae in complex with ADP-ribosyl-L-arginine
ComponentsADP-ribosylhydrolase like 2
KeywordsHYDROLASE / ADP-ribosylation / ADP-ribose / ADPRHL2 / ADP-ribosylhydrolase like 2 / Arg-ADPr / Argenine-ADPr / ADP-Ribosyl-L-arginine
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 / ADP-ribosyl-L-arginine / ADP-ribosylhydrolase ARH3
Similarity search - Component
Biological speciesLatimeria chalumnae (coelacanth)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 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
DepositionAug 24, 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _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)78,41012
Polymers76,5792
Non-polymers1,83010
Water9,386521
1
A: ADP-ribosylhydrolase like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2977
Polymers38,2901
Non-polymers1,0076
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ADP-ribosylhydrolase like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1135
Polymers38,2901
Non-polymers8234
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.145, 96.642, 105.908
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: VAL / Beg label comp-ID: VAL / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 10 - 353 / Label seq-ID: 4 - 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 , 5 types, 531 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-F2R / ADP-ribosyl-L-arginine


Mass: 715.501 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H35N9O15P2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 521 / 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: 2.39 Å3/Da / Density % sol: 48.57 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 200 MM AMMONIUM ACETATE, 25 % (W/V), PEG4000, 100 MM CITRATE PH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.66→71.39 Å / Num. obs: 82067 / % possible obs: 100 % / Redundancy: 8.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.047 / Rrim(I) all: 0.101 / Net I/σ(I): 9.9
Reflection shellResolution: 1.66→1.7 Å / Redundancy: 8.4 % / Rmerge(I) obs: 1.524 / Num. unique obs: 5982 / CC1/2: 0.676 / Rpim(I) all: 0.809 / Rrim(I) all: 1.733 / % 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: 1.66→71.39 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / SU B: 5.959 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18994 4030 4.9 %RANDOM
Rwork0.16855 ---
obs0.16965 77918 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.064 Å2
Baniso -1Baniso -2Baniso -3
1--1.33 Å20 Å20 Å2
2---1.7 Å20 Å2
3---3.04 Å2
Refinement stepCycle: 1 / Resolution: 1.66→71.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5039 0 118 521 5678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0145448
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175021
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.6597370
X-RAY DIFFRACTIONr_angle_other_deg1.0631.64311804
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4795709
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.78822.776263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07415964
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2971529
X-RAY DIFFRACTIONr_chiral_restr0.090.2724
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026088
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02970
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_it1.1421.7022678
X-RAY DIFFRACTIONr_mcbond_other1.141.72676
X-RAY DIFFRACTIONr_mcangle_it1.8182.5413353
X-RAY DIFFRACTIONr_mcangle_other1.8172.5413354
X-RAY DIFFRACTIONr_scbond_it1.6761.9472770
X-RAY DIFFRACTIONr_scbond_other1.6751.9482771
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5972.8273988
X-RAY DIFFRACTIONr_long_range_B_refined4.55221.3766444
X-RAY DIFFRACTIONr_long_range_B_other4.48121.1876392
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 11007 / 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: 1.659→1.702 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 275 -
Rwork0.321 5595 -
obs--98.19 %
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)
12.3838-0.3281-0.27971.5823-0.00140.98350.08860.1420.1647-0.1091-0.0376-0.02450.0115-0.0436-0.0510.07720.00360.01240.1129-0.00420.0273-16.371-11.30410.473
21.6867-0.28660.16371.81640.09671.04140.02060.0798-0.004-0.10630.00510.0154-0.01580.0126-0.02570.0634-0.00260.00880.10320.00650.006910.16211.02110.311
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 769
2X-RAY DIFFRACTION2B9 - 752

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