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- PDB-2pqf: Human Poly(ADP-Ribose) Polymerase 12, Catalytic fragment in compl... -

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Basic information

Entry
Database: PDB / ID: 2pqf
TitleHuman Poly(ADP-Ribose) Polymerase 12, Catalytic fragment in complex with an inhibitor 3-Aminobenzoic acid
ComponentsPoly [ADP-ribose] polymerase 12
KeywordsTRANSFERASE / ENZYME-INHIBITOR COMPLEX / CATALYTIC FRAGMENT / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


NAD+-protein-cysteine ADP-ribosyltransferase activity / protein auto-ADP-ribosylation / NAD+-protein ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+-protein poly-ADP-ribosyltransferase activity / nucleotidyltransferase activity / RNA binding / nucleus / metal ion binding
Similarity search - Function
Zinc finger C-x8-C-x5-C-x3-H type (and similar) / WWE domain / WWE domain superfamily / WWE domain / WWE domain profile. / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 ...Zinc finger C-x8-C-x5-C-x3-H type (and similar) / WWE domain / WWE domain superfamily / WWE domain / WWE domain profile. / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / Winged helix-like DNA-binding domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / 3-AMINOBENZOIC ACID / Protein mono-ADP-ribosyltransferase PARP12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsKarlberg, T. / Lehtio, L. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. ...Karlberg, T. / Lehtio, L. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hogbom, M. / Johansson, I. / Kallas, A. / Kotenyova, T. / Moche, M. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Sundstrom, M. / Thorsell, A.G. / Van Den Berg, S. / Weigelt, J. / Holmberg-Schiavone, L. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Basis for Lack of ADP-ribosyltransferase Activity in Poly(ADP-ribose) Polymerase-13/Zinc Finger Antiviral Protein.
Authors: Karlberg, T. / Klepsch, M. / Thorsell, A.G. / Andersson, C.D. / Linusson, A. / Schuler, H.
History
DepositionMay 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 4, 2015Group: Database references
Revision 1.4Apr 22, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Poly [ADP-ribose] polymerase 12
B: Poly [ADP-ribose] polymerase 12
C: Poly [ADP-ribose] polymerase 12
D: Poly [ADP-ribose] polymerase 12
E: Poly [ADP-ribose] polymerase 12
F: Poly [ADP-ribose] polymerase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,91918
Polymers136,9446
Non-polymers1,97612
Water5,729318
1
A: Poly [ADP-ribose] polymerase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1533
Polymers22,8241
Non-polymers3292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Poly [ADP-ribose] polymerase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1533
Polymers22,8241
Non-polymers3292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Poly [ADP-ribose] polymerase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1533
Polymers22,8241
Non-polymers3292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Poly [ADP-ribose] polymerase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1533
Polymers22,8241
Non-polymers3292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Poly [ADP-ribose] polymerase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1533
Polymers22,8241
Non-polymers3292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Poly [ADP-ribose] polymerase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1533
Polymers22,8241
Non-polymers3292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
C: Poly [ADP-ribose] polymerase 12
hetero molecules

F: Poly [ADP-ribose] polymerase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3066
Polymers45,6482
Non-polymers6594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area2560 Å2
ΔGint-2 kcal/mol
Surface area19240 Å2
MethodPISA
8
B: Poly [ADP-ribose] polymerase 12
hetero molecules

D: Poly [ADP-ribose] polymerase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3066
Polymers45,6482
Non-polymers6594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555y+1/2,-x+1/2,z+1/21
Buried area2460 Å2
ΔGint0 kcal/mol
Surface area18980 Å2
MethodPISA
9
A: Poly [ADP-ribose] polymerase 12
hetero molecules

E: Poly [ADP-ribose] polymerase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3066
Polymers45,6482
Non-polymers6594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area2540 Å2
ΔGint1 kcal/mol
Surface area19150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)206.590, 206.590, 84.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: GLN / End label comp-ID: SER / Refine code: 5 / Auth seq-ID: 499 - 680 / Label seq-ID: 13 - 194

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
DetailsThe biological assembly is a monomer

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Components

#1: Protein
Poly [ADP-ribose] polymerase 12 / PARP-12 / Zinc finger CCCH domain-containing protein 1


Mass: 22823.986 Da / Num. of mol.: 6 / Fragment: catalytic fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP12, ZC3HDC1 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)goldpRARE2 / References: UniProt: Q9H0J9, NAD+ ADP-ribosyltransferase
#2: Chemical
ChemComp-GAB / 3-AMINOBENZOIC ACID / GABACULINE


Mass: 137.136 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H7NO2
#3: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 3.3 Å3/Da / Density % sol: 62.72 %
Crystal growTemperature: 298 K / pH: 4.3
Details: 9% PEG 6000, 100mM Na Citrate, 2% DMSO, pH 4.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 4.30

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97982
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 14, 2007 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97982 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 90498 / % possible obs: 1 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.071 / Rsym value: 0.083 / Net I/σ(I): 12.8
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 3.5 / Rsym value: 0.335 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.3.0032refinement
XDSdata reduction
XSCALEdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→19.6 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.927 / SU B: 11.686 / SU ML: 0.15 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2444 1810 2 %RANDOM
Rwork0.19831 ---
obs0.19922 88683 100 %-
all-88683 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.866 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8995 0 138 318 9451
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0229392
X-RAY DIFFRACTIONr_bond_other_d0.0020.026313
X-RAY DIFFRACTIONr_angle_refined_deg1.5851.91712682
X-RAY DIFFRACTIONr_angle_other_deg0.99315184
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.90951069
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.83923.712493
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.792151457
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.3091548
X-RAY DIFFRACTIONr_chiral_restr0.1340.21279
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210452
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022179
X-RAY DIFFRACTIONr_nbd_refined0.3030.151641
X-RAY DIFFRACTIONr_nbd_other0.1780.156011
X-RAY DIFFRACTIONr_nbtor_refined0.1970.54334
X-RAY DIFFRACTIONr_nbtor_other0.0930.54728
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.3615
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0330.31
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5410.1520
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2080.1546
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2290.38
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9691.55936
X-RAY DIFFRACTIONr_mcbond_other0.2361.52220
X-RAY DIFFRACTIONr_mcangle_it1.25328748
X-RAY DIFFRACTIONr_scbond_it1.82234503
X-RAY DIFFRACTIONr_scangle_it2.6044.53934
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1020medium positional0.280.5
2B1020medium positional0.250
3C1020medium positional0.370
4D1020medium positional0.220
5E1020medium positional0.250
6F1020medium positional0.330
1A1349loose positional0.725
2B1349loose positional0.810
3C1349loose positional0.860
4D1349loose positional0.690
5E1349loose positional0.710
6F1349loose positional0.910
1A1020medium thermal0.812
2B1020medium thermal0.740
3C1020medium thermal1.060
4D1020medium thermal0.980
5E1020medium thermal0.770
6F1020medium thermal0.920
1A1349loose thermal0.7810
2B1349loose thermal0.850.01
3C1349loose thermal1.070
4D1349loose thermal0.950
5E1349loose thermal0.80
6F1349loose thermal0.890
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 131 -
Rwork0.245 6455 -
obs--100 %
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)
15.2902-2.0195-0.86832.0585-0.38272.5560.28580.07410.2932-0.0126-0.1808-0.2577-0.49010.4024-0.1049-0.0276-0.1688-0.01180.03050.0678-0.140295.8552.429-2.409
20.94370.18470.36340.7231-0.47042.2561-0.01050.08280.0024-0.12020.0114-0.04260.32890.1706-0.0008-0.0397-0.081-0.0058-0.0212-0.0068-0.183889.68538.3762.802
31.8241-0.1002-0.25472.5492-1.13591.733-0.10780.0182-0.1603-0.0772-0.0240.02980.37680.05710.1319-0.0012-0.04410.0051-0.0506-0.0279-0.191493.35331.6537.996
45.23463.5757-0.60185.05670.21035.4507-0.06720.22150.1050.0583-0.02760.0606-0.2384-0.59880.0949-0.09040.1223-0.04110.0867-0.0556-0.200997.06451.67844.131
51.8393-0.11590.24530.76861.53373.1852-0.0519-0.1907-0.18110.11060.0685-0.01190.3695-0.1033-0.0166-0.0510.013-0.01570.04150.0029-0.1884106.39440.43238.463
64.9505-0.5954-1.17075.41782.12164.9901-0.14910.1804-0.6576-0.2649-0.1327-0.0760.5682-0.13150.2817-0.04820.0165-0.00690.06190.0672-0.1429104.8332.2832.873
75.31472.15482.73693.790.53614.4375-0.0204-0.14260.3585-0.0388-0.13130.044-0.0024-0.1020.1516-0.151-0.02790.0168-0.0884-0.0012-0.16390.0760.64819.35
82.74550.3292-0.7291.30540.73641.47930.0168-0.26860.04550.15720.05470.11560.0801-0.0855-0.0714-0.09170.0275-0.0036-0.053-0.0015-0.086778.15662.7629.819
92.2530.5589-1.41651.0384-0.3412.3657-0.0991-0.23290.02750.11550.16860.09270.0838-0.1694-0.0696-0.09880.04380.00690.01920.0622-0.117772.09756.33634.238
102.51870.8164-0.05111.6261-1.87522.53840.03460.03920.20950.14280.08060.1604-0.1939-0.0682-0.1152-0.0087-0.0973-0.0188-0.05230.0182-0.190561.33231.58519.088
111.59020.61371.61483.1066-1.63243.41260.10660.194-0.0928-0.2087-0.0062-0.13360.36960.2967-0.10050.0417-0.0869-0.0194-0.0179-0.0182-0.191667.00417.68224.144
125.38610.36450.98483.86870.25153.148-0.0995-0.2854-0.5330.2280.2296-0.36140.46760.3262-0.13010.0058-0.01590.01720.0193-0.1154-0.155974.43815.60328.948
132.35211.1615-0.37444.61440.34792.5001-0.15620.21950.17090.06940.16070.32940.1705-0.4694-0.0045-0.0261-0.11120.0464-0.0193-0.0159-0.182861.40832.50264.354
141.55830.6453-1.0692.32250.7523.8775-0.0269-0.1408-0.0470.20620.0002-0.0820.2850.19490.0268-0.0115-0.0682-0.0253-0.05310.004-0.202576.5430.8959.748
153.4305-0.3186-0.87664.9211-0.5082.04740.04990.0596-0.1109-0.3159-0.2816-0.58830.28950.27390.23170.01320.0008-0.0226-0.03620.0442-0.15281.12124.19754.473
162.6338-0.8349-0.03241.5881-0.69882.0090.0079-0.10930.27530.16690.0369-0.11160.00530.1113-0.0447-0.0696-0.0860.0346-0.0912-0.0599-0.1019108.38768.46724.068
174.1107-0.1945-1.41574.4848-0.8682.17280.03650.24840.3088-0.06430.0881-0.0120.05160.3203-0.1247-0.0802-0.03640.028-0.03270.0338-0.0287120.21865.97613.936
182.2831-0.5209-1.28691.29080.99641.1468-0.0980.18420.1305-0.08570.152400.04170.3883-0.0544-0.02180.026-0.02110.0846-0.0271-0.152122.98558.0878.439
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA496 - 53010 - 44
2X-RAY DIFFRACTION2AA531 - 62445 - 138
3X-RAY DIFFRACTION3AA625 - 681139 - 195
4X-RAY DIFFRACTION4BB495 - 5309 - 44
5X-RAY DIFFRACTION5BB531 - 62445 - 138
6X-RAY DIFFRACTION6BB625 - 680139 - 194
7X-RAY DIFFRACTION7CC496 - 53010 - 44
8X-RAY DIFFRACTION8CC531 - 62445 - 138
9X-RAY DIFFRACTION9CC625 - 680139 - 194
10X-RAY DIFFRACTION10DD496 - 53010 - 44
11X-RAY DIFFRACTION11DD531 - 62445 - 138
12X-RAY DIFFRACTION12DD625 - 681139 - 195
13X-RAY DIFFRACTION13EE496 - 53010 - 44
14X-RAY DIFFRACTION14EE531 - 62445 - 138
15X-RAY DIFFRACTION15EE625 - 680139 - 194
16X-RAY DIFFRACTION16FF496 - 53010 - 44
17X-RAY DIFFRACTION17FF531 - 62445 - 138
18X-RAY DIFFRACTION18FF625 - 680139 - 194

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