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- PDB-5lw0: Oryza sativa APL macrodomain in complex with ADP-ribose -

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Basic information

Entry
Database: PDB / ID: 5lw0
TitleOryza sativa APL macrodomain in complex with ADP-ribose
ComponentsBasic helix-loop-helix, putative, expressed
KeywordsADP-RIBOSE-BINDING PROTEIN / ADP-ribosyltransferase / Interstrand crosslink repair
Function / homology
Function and homology information


Aprataxin, C2HE/C2H2/C2HC zinc finger / C2HE / C2H2 / C2HC zinc-binding finger / Scavenger mRNA decapping enzyme C-term binding / AAA domain / Histidine triad, conserved site / HIT domain signature. / HIT-like superfamily / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. ...Aprataxin, C2HE/C2H2/C2HC zinc finger / C2HE / C2H2 / C2HC zinc-binding finger / Scavenger mRNA decapping enzyme C-term binding / AAA domain / Histidine triad, conserved site / HIT domain signature. / HIT-like superfamily / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-AR6 / GLYCINE / PHOSPHATE ION / Macro domain-containing protein / Basic helix-loop-helix, putative, expressed
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsAriza, A.
Funding support United Kingdom, 5items
OrganizationGrant numberCountry
Cancer Research UKC1521/A12353 United Kingdom
Medical Research Council (United Kingdom)MR/L000164/1 United Kingdom
NC3RsNC/K00137X/1 United Kingdom
Wellcome Trust101794 United Kingdom
European Research Council281739 United Kingdom
CitationJournal: J.Cell.Sci. / Year: 2016
Title: The role of ADP-ribosylation in regulating DNA interstrand crosslink repair.
Authors: Gunn, A.R. / Banos-Pinero, B. / Paschke, P. / Sanchez-Pulido, L. / Ariza, A. / Day, J. / Emrich, M. / Leys, D. / Ponting, C.P. / Ahel, I. / Lakin, N.D.
History
DepositionSep 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 2.0Sep 13, 2017Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
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 / _pdbx_audit_support.funding_organization
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_contact_author / pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Basic helix-loop-helix, putative, expressed
B: Basic helix-loop-helix, putative, expressed
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3279
Polymers50,7742
Non-polymers1,5547
Water6,575365
1
A: Basic helix-loop-helix, putative, expressed
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1364
Polymers25,3871
Non-polymers7493
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Basic helix-loop-helix, putative, expressed
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1915
Polymers25,3871
Non-polymers8044
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.496, 91.318, 62.882
Angle α, β, γ (deg.)90.00, 103.32, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-589-

HOH

21B-590-

HOH

31B-592-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A29 - 229
2010B29 - 229

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Components

#1: Protein Basic helix-loop-helix, putative, expressed / APL


Mass: 25386.852 Da / Num. of mol.: 2 / Fragment: UNP residues 78-296
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: LOC_Os03g18210 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q10MW4, UniProt: B8ALM5*PLUS
#2: 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
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.32 Å3/Da / Density % sol: 46.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 25% PEG 1500 + 0.1 M SPG buffer (succinic acid, sodium phosphate monobasic monohydrate and glycine)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 7, 2015
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.65→56.31 Å / Num. obs: 47191 / % possible obs: 97.4 % / Redundancy: 6.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.8
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 3.2 / CC1/2: 0.875 / % possible all: 77.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LW6

5lw6


Resolution: 1.65→56.31 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.788 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.091 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18727 2344 5 %RANDOM
Rwork0.15477 ---
obs0.1564 44846 97.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.533 Å2
Baniso -1Baniso -2Baniso -3
1--1.37 Å20 Å20.31 Å2
2--0.14 Å2-0 Å2
3---0.97 Å2
Refinement stepCycle: LAST / Resolution: 1.65→56.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3113 0 97 365 3575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0193373
X-RAY DIFFRACTIONr_bond_other_d0.0060.023248
X-RAY DIFFRACTIONr_angle_refined_deg1.5641.9944613
X-RAY DIFFRACTIONr_angle_other_deg0.95837497
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9655440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.80123.916143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55315575
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2141525
X-RAY DIFFRACTIONr_chiral_restr0.1010.2538
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213800
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02761
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_it2.3192.0751666
X-RAY DIFFRACTIONr_mcbond_other2.2772.061659
X-RAY DIFFRACTIONr_mcangle_it3.3553.0932085
X-RAY DIFFRACTIONr_mcangle_other3.3573.0852082
X-RAY DIFFRACTIONr_scbond_it3.9572.5841707
X-RAY DIFFRACTIONr_scbond_other3.9572.5841707
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9393.6762510
X-RAY DIFFRACTIONr_long_range_B_refined7.9418.854173
X-RAY DIFFRACTIONr_long_range_B_other7.87118.2983994
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 12699 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 120 -
Rwork0.224 2734 -
obs--79.68 %

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