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- PDB-6hh3: ADP-ribosylserine hydrolase ARH3 of Latimeria chalumnae in comple... -

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Basic information

Entry
Database: PDB / ID: 6hh3
TitleADP-ribosylserine hydrolase ARH3 of Latimeria chalumnae in complex with ADP-HPD
ComponentsADP-ribosylhydrolase like 2
KeywordsHYDROLASE / ADP-ribosylation / ADP-ribose / ADPRHL2 / ADP-ribosylhydrolase like 2 / ADP-HPD
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
Chem-A1R / ADP-ribosylhydrolase ARH3
Similarity search - Component
Biological speciesLatimeria chalumnae (coelacanth)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 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 / 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_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_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.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)77,94510
Polymers76,5792
Non-polymers1,3668
Water4,666259
1
A: ADP-ribosylhydrolase like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9735
Polymers38,2901
Non-polymers6834
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ADP-ribosylhydrolase like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9735
Polymers38,2901
Non-polymers6834
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.850, 98.248, 105.624
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: PRO / Beg label comp-ID: PRO / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 8 - 353 / Label seq-ID: 2 - 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.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-A1R / 5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]ADENOSINE


Mass: 542.332 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N6O12P2
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.41 Å3/Da / Density % sol: 48.86 %
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: 1.82→44.55 Å / Num. obs: 63174 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.042 / Rrim(I) all: 0.109 / Net I/σ(I): 11.2
Reflection shellResolution: 1.82→1.87 Å / Redundancy: 12.7 % / Rmerge(I) obs: 2.242 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4589 / CC1/2: 0.875 / Rpim(I) all: 0.941 / Rrim(I) all: 2.434 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
PDB_EXTRACT3.22data extraction
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FOZ

2foz


Resolution: 1.82→44.54 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.963 / SU B: 8.764 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21005 3174 5 %RANDOM
Rwork0.17912 ---
obs0.18072 59898 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.72 Å2
Baniso -1Baniso -2Baniso -3
1--2.15 Å2-0 Å2-0 Å2
2--0.6 Å2-0 Å2
3---1.55 Å2
Refinement stepCycle: 1 / Resolution: 1.82→44.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5057 0 86 259 5402
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0145353
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174910
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.6747232
X-RAY DIFFRACTIONr_angle_other_deg0.9911.65111517
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5255687
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.73523.02255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.86815930
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2931528
X-RAY DIFFRACTIONr_chiral_restr0.0740.2706
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025964
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02966
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_it1.5732.8372658
X-RAY DIFFRACTIONr_mcbond_other1.5732.8372657
X-RAY DIFFRACTIONr_mcangle_it2.4944.2433324
X-RAY DIFFRACTIONr_mcangle_other2.4944.2433325
X-RAY DIFFRACTIONr_scbond_it2.0133.1472695
X-RAY DIFFRACTIONr_scbond_other2.0123.1472695
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1134.6013892
X-RAY DIFFRACTIONr_long_range_B_refined4.54233.6996116
X-RAY DIFFRACTIONr_long_range_B_other4.46633.6396101
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 10872 / 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: 1.818→1.865 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 217 -
Rwork0.348 4205 -
obs--95.98 %
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)
11.11170.19350.0881.07760.07950.65090.0179-0.0019-0.09930.0831-0.055-0.0024-0.0144-0.03520.0370.0213-0.01640.0110.1942-0.05020.1334-10.1311.247-9.999
23.45260.8805-0.64841.4268-0.03350.91210.1905-0.34170.3450.0709-0.04970.10770.060.1522-0.14080.0256-0.0130.01810.23980.07980.155416.178-11.75-10.644
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 601
2X-RAY DIFFRACTION2B8 - 601

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