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- PDB-8xpx: The Crystal Structure of PARP12 from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8xpx
TitleThe Crystal Structure of PARP12 from Biortus.
ComponentsProtein mono-ADP-ribosyltransferase PARP12
KeywordsTRANSFERASE / Glycosyltransferase / Nucleotidyltransferase / Metal-binding
Function / homology
Function and homology information


NAD+-protein-cysteine ADP-ribosyltransferase activity / protein auto-ADP-ribosylation / NAD+-protein ADP-ribosyltransferase activity / NAD+-protein poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleotidyltransferase activity / RNA binding / nucleus / metal ion binding
Similarity search - Function
: / WWE domain / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / WWE domain superfamily / WWE domain / WWE domain profile. / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Poly(ADP-ribose) polymerase catalytic domain ...: / WWE domain / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / WWE domain superfamily / WWE domain / WWE domain profile. / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / Protein mono-ADP-ribosyltransferase PARP12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsWang, F. / Cheng, W. / Lv, Z. / Qi, J. / Shen, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of PARP12 from Biortus.
Authors: Wang, F. / Cheng, W. / Lv, Z. / Qi, J. / Shen, Z.
History
DepositionJan 4, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein mono-ADP-ribosyltransferase PARP12
B: Protein mono-ADP-ribosyltransferase PARP12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,54413
Polymers44,7942
Non-polymers75011
Water5,405300
1
A: Protein mono-ADP-ribosyltransferase PARP12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8638
Polymers22,3971
Non-polymers4667
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein mono-ADP-ribosyltransferase PARP12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6805
Polymers22,3971
Non-polymers2834
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.940, 74.930, 61.490
Angle α, β, γ (deg.)90.000, 113.835, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein mono-ADP-ribosyltransferase PARP12 / ADP-ribosyltransferase diphtheria toxin-like 12 / ARTD12 / Poly [ADP-ribose] polymerase 12 / PARP- ...ADP-ribosyltransferase diphtheria toxin-like 12 / ARTD12 / Poly [ADP-ribose] polymerase 12 / PARP-12 / Zinc finger CCCH domain-containing protein 1


Mass: 22396.975 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP12, ZC3HDC1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9H0J9, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.21 Å3/Da / Density % sol: 44.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M NH4Ac, 0.1M Na3 Citrate pH5.2, 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→46.6 Å / Num. obs: 38860 / % possible obs: 98.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 10.8
Reflection shellResolution: 1.75→1.78 Å / Rmerge(I) obs: 0.728 / Num. unique obs: 2153

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→46.6 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.495 / SU ML: 0.077 / Cross valid method: FREE R-VALUE / ESU R: 0.11 / ESU R Free: 0.104
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1942 1898 4.884 %
Rwork0.1636 36961 -
all0.165 --
obs-38859 98.69 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.829 Å2
Baniso -1Baniso -2Baniso -3
1--1.141 Å20 Å20.366 Å2
2--0.068 Å2-0 Å2
3---0.539 Å2
Refinement stepCycle: LAST / Resolution: 1.75→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2970 0 50 300 3320
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0123134
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162825
X-RAY DIFFRACTIONr_angle_refined_deg1.1161.6624236
X-RAY DIFFRACTIONr_angle_other_deg0.3961.5846479
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2375371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.273516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.44110491
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.74410164
X-RAY DIFFRACTIONr_chiral_restr0.0570.2432
X-RAY DIFFRACTIONr_chiral_restr_other0.0510.22
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023762
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02834
X-RAY DIFFRACTIONr_nbd_refined0.2050.2527
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.22443
X-RAY DIFFRACTIONr_nbtor_refined0.1880.21494
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21523
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2232
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1320.219
X-RAY DIFFRACTIONr_nbd_other0.1440.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1170.236
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0040.21
X-RAY DIFFRACTIONr_mcbond_it2.1422.7741467
X-RAY DIFFRACTIONr_mcbond_other2.1162.7681460
X-RAY DIFFRACTIONr_mcangle_it3.3424.9481821
X-RAY DIFFRACTIONr_mcangle_other3.3414.951822
X-RAY DIFFRACTIONr_scbond_it2.8183.1671667
X-RAY DIFFRACTIONr_scbond_other2.8173.1671668
X-RAY DIFFRACTIONr_scangle_it4.5475.6242409
X-RAY DIFFRACTIONr_scangle_other4.5465.6242410
X-RAY DIFFRACTIONr_lrange_it6.43531.0243548
X-RAY DIFFRACTIONr_lrange_other6.33428.9763477
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.75-1.7950.3271290.26727450.26928890.9380.95299.48080.249
1.795-1.8450.31320.24826690.25128240.9480.95999.18550.225
1.845-1.8980.2411480.21925580.2227400.9640.96898.75910.192
1.898-1.9560.2141560.20724760.20826680.970.97298.65070.181
1.956-2.020.2071280.17824530.1826000.9730.97999.26920.153
2.02-2.0910.1811190.17723600.17724940.9780.9899.39860.156
2.091-2.170.191110.16422720.16524030.9770.98399.16770.145
2.17-2.2580.21930.15622050.15823220.9730.98598.96640.14
2.258-2.3580.1841070.14521070.14722540.980.98698.22540.13
2.358-2.4730.1651020.14819950.14921370.9850.98798.12820.138
2.473-2.6070.2181240.15618920.15920370.9720.98698.96910.147
2.607-2.7640.2930.15817980.1619190.9760.98498.54090.152
2.764-2.9540.189920.15516910.15718050.9780.98598.78120.153
2.954-3.190.196780.1515870.15216870.9790.98798.69590.152
3.19-3.4930.172700.15414450.15515490.9810.98797.8050.165
3.493-3.9020.167750.14613150.14814120.9860.98898.44190.16
3.902-4.5010.157530.12911710.13112520.9870.98997.76360.147
4.501-5.4990.148320.14510140.14510700.9880.98997.7570.169
5.499-7.7230.269270.2027740.2048280.9740.98296.73910.232
7.723-46.5460.244290.2214340.2224830.9710.96995.85920.293

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