[English] 日本語
Yorodumi
- PDB-5ldq: Crystal structure of E.coli LigT complexed with NADP+ -

+
Open data


ID or keywords:

Loading...

-
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 / RNA 2',3'-cyclic 3'-phosphodiesterase activity / 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity / ATP binding
Similarity search - Function
2'-5' RNA ligase superfamily / RNA 2',3'-cyclic phosphodiesterase / 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
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more