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- PDB-5ldq: Crystal structure of E.coli LigT complexed with NADP+ -

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Basic information

Entry
Database: PDB / ID: 5ldq
TitleCrystal structure of E.coli LigT complexed with NADP+
ComponentsRNA 2',3'-cyclic phosphodiesterase
KeywordsHYDROLASE / Enzyme / 2H phosphoesterase/ligase
Function / homology
Function and homology information


RNA 2',3'-cyclic 3'-phosphodiesterase / 2'-5'-RNA ligase activity / 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity / ATP binding
Similarity search - Function
RNA 2',3'-cyclic phosphodiesterase / Phosphoesterase, HXTX / LigT like Phosphoesterase / Cyclic Phosphodiesterase; Chain: A, / Cyclic phosphodiesterase / Cyclic phosphodiesterase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / PHOSPHATE ION / RNA 2',3'-cyclic phosphodiesterase
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMyllykoski, M. / Kursula, P.
CitationJournal: PLoS ONE / Year: 2017
Title: Structural aspects of nucleotide ligand binding by a bacterial 2H phosphoesterase.
Authors: Myllykoski, M. / Kursula, P.
History
DepositionJun 27, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Database references
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA 2',3'-cyclic phosphodiesterase
B: RNA 2',3'-cyclic phosphodiesterase
C: RNA 2',3'-cyclic phosphodiesterase
D: RNA 2',3'-cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,81316
Polymers80,1804
Non-polymers4,63312
Water11,494638
1
A: RNA 2',3'-cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8065
Polymers20,0451
Non-polymers1,7614
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA 2',3'-cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0624
Polymers20,0451
Non-polymers1,0173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNA 2',3'-cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0624
Polymers20,0451
Non-polymers1,0173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: RNA 2',3'-cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8833
Polymers20,0451
Non-polymers8382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.740, 91.620, 120.610
Angle α, β, γ (deg.)90.00, 102.31, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
RNA 2',3'-cyclic phosphodiesterase / RNA 2' / 3'-CPDase


Mass: 20045.029 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Gene: thpR, ECBD_3472 / Plasmid: pTH 27 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A140NFI1, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases

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Non-polymers , 5 types, 650 molecules

#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 638 / 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: 2.92 Å3/Da / Density % sol: 57.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.1 M Tris-HCl pH 7.4, 0.2 M MgCl2, 20% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.03 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.7→120 Å / Num. obs: 100969 / % possible obs: 99.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 27.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Net I/σ(I): 13.92
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 3.86 % / Rmerge(I) obs: 1.043 / Mean I/σ(I) obs: 1.23 / CC1/2: 0.619 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBid:5ldi
Resolution: 1.7→117.835 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.5
RfactorNum. reflection% reflectionSelection details
Rfree0.2126 1998 1.98 %Random selection
Rwork0.1834 ---
obs0.1839 100858 99.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 39.45 Å2
Refinement stepCycle: LAST / Resolution: 1.7→117.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5555 0 255 638 6448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076635
X-RAY DIFFRACTIONf_angle_d1.3219118
X-RAY DIFFRACTIONf_dihedral_angle_d19.6232568
X-RAY DIFFRACTIONf_chiral_restr0.09949
X-RAY DIFFRACTIONf_plane_restr0.0041165
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6999-1.74240.41661390.38326928X-RAY DIFFRACTION99
1.7424-1.78960.42041430.33577020X-RAY DIFFRACTION100
1.7896-1.84220.34421420.30057038X-RAY DIFFRACTION100
1.8422-1.90170.32241420.27457022X-RAY DIFFRACTION100
1.9017-1.96970.30821440.2487113X-RAY DIFFRACTION100
1.9697-2.04850.24191420.20997019X-RAY DIFFRACTION100
2.0485-2.14180.25721410.1947002X-RAY DIFFRACTION100
2.1418-2.25470.22371440.18367118X-RAY DIFFRACTION100
2.2547-2.3960.21781420.18457045X-RAY DIFFRACTION100
2.396-2.5810.21171430.18697070X-RAY DIFFRACTION100
2.581-2.84070.22871430.18287091X-RAY DIFFRACTION100
2.8407-3.25180.20341430.17347067X-RAY DIFFRACTION100
3.2518-4.0970.17011440.15287140X-RAY DIFFRACTION100
4.097-118.11880.17011460.15667187X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.2057-0.34550.7713.6364-3.57965.62960.2454-0.29890.17970.2328-0.07920.34450.2793-0.2897-0.14260.1826-0.12120.05540.2125-0.040.232111.5576-9.938954.9224
27.76495.04262.27193.46531.22963.622-0.43580.20240.4761-0.84410.35331.0516-0.0688-0.61620.15420.2187-0.0431-0.11190.26850.02480.26255.6166-14.273733.8644
32.84031.652.29832.18391.87863.98950.1595-0.19630.1060.1855-0.20350.28840.2217-0.3890.04820.2024-0.08650.01690.19640.00470.20846.6227-17.829248.575
43.45063.0922-2.82678.0518-0.234.80090.4537-0.79780.21540.8741-0.3372-0.2282-0.18350.3108-0.21260.1667-0.0678-0.08320.3594-0.01160.239121.0934-4.669463.1323
50.86460.15920.05851.61110.29283.1267-0.1242-0.0268-0.2017-0.2270.0824-0.18520.36640.07270.0270.15760.024-0.00380.14670.01460.183918.2938-19.722441.9509
65.0194-0.9164-3.30917.19351.09182.39470.1198-0.3649-0.11460.7981-0.0542-0.51790.63881.1036-0.05590.26190.0092-0.09340.24590.0230.273926.0906-14.514854.6441
70.2-0.2153-0.3220.71140.79040.91940.3924-1.2339-0.16121.2966-0.1199-0.1231.7410.2194-0.23130.7055-0.0681-0.08210.6050.04040.317520.3009-22.075855.5191
87.09843.9061.94197.15432.38623.15460.0408-0.3207-0.62430.5059-0.2117-0.15061.1602-0.40410.19970.4171-0.13350.02750.26910.02160.23765.0284-25.614645.0523
90.3513-0.18230.17462.66130.59561.86890.0153-0.1157-0.0941-0.0982-0.22860.22450.4633-0.60530.11320.184-0.1390.01680.3385-0.0260.218210.811-13.94842.6998
106.82561.9214-0.38086.04030.66523.2490.13350.07380.2648-0.1011-0.04250.15380.189-0.2426-0.03950.0986-0.0278-0.05610.21330.02970.16614.8896-4.602850.6209
114.01050.20011.20952.52910.76443.41050.05320.06750.78420.2750.03380.0802-0.90370.0415-0.00280.3289-0.01520.08030.16390.02760.3578-1.7425-19.922376.9546
125.1907-1.2927-5.09292.89742.21326.58850.0055-0.31060.69430.44070.135-0.83380.11450.8177-0.12260.06050.007-0.10630.3070.04940.37511.5544-37.493674.4543
133.1698-2.9956-3.4364.12741.66115.85520.4239-0.50520.2473-0.87790.0066-1.3695-0.60451.0781-0.30010.1734-0.03270.10330.48230.06150.457715.1856-28.955665.1989
147.0678-2.6334-0.04797.4661.29061.8451-0.01750.31140.36540.4078-0.05380.05-0.81170.24830.08140.3288-0.0280.02610.17610.08080.1865-0.4622-21.655474.0405
157.00575.069-1.67657.8565-2.06527.64680.36750.10721.5813-0.10.08861.0231-1.1226-0.3058-0.40190.42410.15940.01980.2819-0.00890.5075-13.5274-14.920881.3227
162.0841-2.3156-0.89452.92651.19560.4708-0.09410.1636-0.1678-0.3045-0.1180.2609-0.1508-0.55660.0069-0.06250.1053-0.04910.3166-0.0230.2983-9.421-35.897177.4545
176.40134.4897-2.26025.06960.12012.595-0.0190.19920.0637-0.71070.02810.2127-0.306-0.0901-0.06680.17630.0489-0.06630.19430.00420.21670.7826-34.086162.9659
188.2602-4.3413-0.70094.2765-1.42798.01370.07170.62570.4912-0.4347-0.1520.9853-0.5677-1.3784-0.00930.2550.1255-0.04240.40010.04980.2733-14.1617-26.606771.9789
197.02-4.1471-3.13864.57313.89143.38080.36870.59281.0267-0.5466-0.32780.262-2.1225-0.8785-0.17580.64250.20120.0260.44350.02240.4358-8.7033-24.307666.5038
207.86711.4376-4.45335.54850.69263.04220.21660.2880.31-0.9520.0826-0.3974-0.69410.0774-0.30890.3147-0.0230.06410.25870.05940.27199.5975-27.897862.4993
211.5287-0.661-1.09693.3295-0.27042.3190.05490.01290.06840.0566-0.1015-0.3421-0.23490.17220.05380.1235-0.005-0.06290.20050.02460.21363.4587-31.366873.8633
222.80674.6922-2.85788.9476-2.98487.4838-0.0896-0.0484-0.02930.11630.0733-0.0544-0.41280.01170.03370.16020.0771-0.00660.1809-0.00740.1461-4.3327-24.657482.6045
232.19-1.21051.00374.547-0.67972.7702-0.11950.0937-0.1828-0.29970.14320.41670.5915-0.2959-0.08370.3112-0.07980.00220.2316-0.00630.218513.3886-16.372513.4645
246.6914.58640.72234.12781.06870.43750.327-0.3924-0.8870.4149-0.0778-0.54451.67040.2096-0.23381.10040.13090.0310.30490.03680.435124.8435-33.443126.8605
251.3886-0.8229-0.03581.8775-0.45230.13440.03420.0683-0.0507-0.7045-0.1314-0.18420.44860.1163-0.0660.36430.00360.01930.1885-0.00410.211224.5159-12.984610.1873
265.0347-1.29270.85772.52521.12055.1046-0.37990.2427-0.6879-0.25590.1456-1.36661.09271.45020.02330.42890.1970.12160.50040.01230.37531.8399-23.01819.0279
272.79340.52570.74150.8703-0.27544.68120.04460.1847-0.511-0.91290.04270.07930.70370.446-0.08630.5010.00860.02590.2435-0.03560.281820.7943-15.90137.1216
280.7244-0.6889-1.10473.50210.65412.9244-0.10880.2437-0.043-0.5272-0.02120.61090.5991-0.29530.11220.4304-0.1009-0.04030.2142-0.02140.2715.0195-20.360819.692
298.44622.18372.83346.46831.20196.6929-0.14350.29810.1843-0.0583-0.01570.41580.35450.03150.14960.2525-0.01880.03360.1519-0.01050.148318.2237-21.117725.2275
302.8611-0.4302-1.51333.80641.63124.95290.1650.14350.0744-0.6198-0.34080.3579-0.2399-0.83190.1830.27780.0248-0.04980.301-0.02280.2135-26.0702-29.700212.594
318.7721.87193.17014.0946-1.77253.26540.13040.5671-0.2515-1.6949-0.0925-0.7780.30150.91780.02210.74840.03780.28490.3369-0.01030.431-10.1323-42.6628-0.5261
321.92850.1065-0.6222.13331.74862.82420.0842-0.1380.0998-0.19570.0035-0.26-0.60910.0598-0.01520.2153-0.0820.00010.23740.01590.2062-15.8218-27.798219.4221
336.0029-1.01211.85868.781-0.16623.4766-0.17970.6987-0.0489-0.93490.0083-1.4221-0.6081.90740.13920.2463-0.16460.09520.48080.0190.5889-6.0809-34.414410.667
343.4418-0.82-1.78840.73911.64733.80510.56591.73091.2153-2.557-0.0004-1.4635-1.23750.8561-0.42350.9517-0.08280.30380.7490.15380.6833-10.2069-26.43998.4963
351.3913-0.0473-0.42974.12021.4724.50210.1447-0.02550.1862-0.4072-0.19620.2386-0.5881-0.6640.0650.26760.04050.00220.2708-0.00730.2154-24.6232-27.581115.1023
367.557-2.68973.58892.9478-2.77428.2732-0.2616-0.03010.21880.0078-0.042-0.1967-0.1096-0.3110.0570.2719-0.0439-0.04370.23120.0020.2366-21.353-40.17468.0082
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 14 )
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 28 )
3X-RAY DIFFRACTION3chain 'A' and (resid 29 through 53 )
4X-RAY DIFFRACTION4chain 'A' and (resid 54 through 66 )
5X-RAY DIFFRACTION5chain 'A' and (resid 67 through 96 )
6X-RAY DIFFRACTION6chain 'A' and (resid 97 through 112 )
7X-RAY DIFFRACTION7chain 'A' and (resid 113 through 125 )
8X-RAY DIFFRACTION8chain 'A' and (resid 126 through 134 )
9X-RAY DIFFRACTION9chain 'A' and (resid 135 through 162 )
10X-RAY DIFFRACTION10chain 'A' and (resid 163 through 176 )
11X-RAY DIFFRACTION11chain 'B' and (resid 3 through 14 )
12X-RAY DIFFRACTION12chain 'B' and (resid 15 through 28 )
13X-RAY DIFFRACTION13chain 'B' and (resid 29 through 38 )
14X-RAY DIFFRACTION14chain 'B' and (resid 39 through 53 )
15X-RAY DIFFRACTION15chain 'B' and (resid 54 through 66 )
16X-RAY DIFFRACTION16chain 'B' and (resid 67 through 77 )
17X-RAY DIFFRACTION17chain 'B' and (resid 78 through 96 )
18X-RAY DIFFRACTION18chain 'B' and (resid 97 through 111 )
19X-RAY DIFFRACTION19chain 'B' and (resid 112 through 125 )
20X-RAY DIFFRACTION20chain 'B' and (resid 126 through 134 )
21X-RAY DIFFRACTION21chain 'B' and (resid 135 through 162 )
22X-RAY DIFFRACTION22chain 'B' and (resid 163 through 176 )
23X-RAY DIFFRACTION23chain 'C' and (resid 2 through 53 )
24X-RAY DIFFRACTION24chain 'C' and (resid 54 through 66 )
25X-RAY DIFFRACTION25chain 'C' and (resid 67 through 96 )
26X-RAY DIFFRACTION26chain 'C' and (resid 97 through 112 )
27X-RAY DIFFRACTION27chain 'C' and (resid 113 through 145 )
28X-RAY DIFFRACTION28chain 'C' and (resid 146 through 162 )
29X-RAY DIFFRACTION29chain 'C' and (resid 163 through 176 )
30X-RAY DIFFRACTION30chain 'D' and (resid 2 through 53 )
31X-RAY DIFFRACTION31chain 'D' and (resid 54 through 66 )
32X-RAY DIFFRACTION32chain 'D' and (resid 67 through 96 )
33X-RAY DIFFRACTION33chain 'D' and (resid 97 through 112 )
34X-RAY DIFFRACTION34chain 'D' and (resid 113 through 125 )
35X-RAY DIFFRACTION35chain 'D' and (resid 126 through 162 )
36X-RAY DIFFRACTION36chain 'D' and (resid 163 through 176 )

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