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- PDB-5ldj: Crystal structure of E.coli LigT complexed with phosphate -

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Basic information

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


2'-5'-RNA ligase activity / RNA 2',3'-cyclic 3'-phosphodiesterase / 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
PHOSPHATE ION / RNA 2',3'-cyclic phosphodiesterase
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.802 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 1.2Jan 17, 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)80,6559
Polymers80,1804
Non-polymers4755
Water37821
1
A: RNA 2',3'-cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1402
Polymers20,0451
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA 2',3'-cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1402
Polymers20,0451
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNA 2',3'-cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1402
Polymers20,0451
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: RNA 2',3'-cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2353
Polymers20,0451
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.730, 63.520, 67.370
Angle α, β, γ (deg.)106.26, 106.14, 103.06
Int Tables number1
Space group name H-MP1

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Components

#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
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.54 Å3/Da / Density % sol: 51.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Tris-HCl pH 7.5, 0.2 M MgCl2, 18% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 18651 / % possible obs: 95.7 % / Redundancy: 2.21 % / Biso Wilson estimate: 42.6 Å2 / CC1/2: 0.978 / Rmerge(I) obs: 0.126 / Net I/σ(I): 7.21
Reflection shellResolution: 2.8→2.88 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.942 / Mean I/σ(I) obs: 1.02 / % possible all: 94.3

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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: 2.802→22.956 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 29.09
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1859 9.97 %Random selection
Rwork0.2177 ---
obs0.2218 18643 96.24 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 60.8 Å2
Refinement stepCycle: LAST / Resolution: 2.802→22.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5412 0 25 21 5458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035624
X-RAY DIFFRACTIONf_angle_d0.7057657
X-RAY DIFFRACTIONf_dihedral_angle_d11.5382078
X-RAY DIFFRACTIONf_chiral_restr0.028820
X-RAY DIFFRACTIONf_plane_restr0.003991
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8023-2.8780.40781440.34361279X-RAY DIFFRACTION95
2.878-2.96250.3791330.33121290X-RAY DIFFRACTION96
2.9625-3.05790.33261490.29811313X-RAY DIFFRACTION97
3.0579-3.16690.31191510.28121285X-RAY DIFFRACTION97
3.1669-3.29340.31981420.26811292X-RAY DIFFRACTION98
3.2934-3.44280.311380.26751329X-RAY DIFFRACTION98
3.4428-3.62360.27441490.22431292X-RAY DIFFRACTION97
3.6236-3.84970.30831360.24921235X-RAY DIFFRACTION92
3.8497-4.14530.2471420.18791309X-RAY DIFFRACTION97
4.1453-4.55950.20811470.16361298X-RAY DIFFRACTION96
4.5595-5.21250.18781480.15261291X-RAY DIFFRACTION97
5.2125-6.5420.21461390.18761316X-RAY DIFFRACTION98
6.542-22.95670.17741410.16241255X-RAY DIFFRACTION93
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)
13.4121-0.9690.76874.6424-1.33291.29920.20550.0075-0.0159-0.29890.03440.56220.089-0.1915-0.16630.287-0.03420.00920.29490.00340.2887-3.784991.7477-6.5588
25.483-0.4031.88734.06621.58613.3308-0.14720.1115-0.62530.26310.51010.450.3444-0.4397-0.35570.45-0.1121-0.04140.38410.14380.44381.782585.0312-0.2321
35.7432-0.04670.69233.9975-1.27295.1501-0.190.3604-0.2131-0.8940.21120.56290.1774-0.0882-0.14590.3783-0.0276-0.06690.21420.01150.5046-3.369595.769-14.6448
43.25620.57071.60446.758-0.70143.7296-0.23530.2253-0.4008-1.34620.353-0.82050.29590.7693-0.22130.41230.08470.09490.4621-0.01390.34376.4995114.5273-26.9356
51.3654-0.66051.18843.2901-0.48883.5799-0.1367-0.02630.1644-0.20930.08640.2222-0.4068-0.2030.01030.26010.0039-0.08830.3733-0.01490.4336-1.434124.9072-19.6285
62.23031.81820.40033.7595-0.74565.6651-0.2270.37860.2401-1.13260.21081.0636-0.1363-0.19-0.13820.53970.0944-0.18380.29530.01810.4740.4336118.1049-24.9157
77.2418-0.0897-1.56148.1072.59187.3844-0.12220.39180.5911-0.6426-0.1998-0.4785-0.66670.12760.11210.3472-0.0066-0.12340.19340.09690.394810.3599126.2179-19.5762
84.50921.8082-0.7244.8259-1.06842.50720.2487-0.8604-1.45260.23710.0632-0.55310.34040.19060.37420.8693-0.1118-0.46240.27110.2350.3687-18.7054113.3215-44.336
96.88883.0641-1.53686.150.97242.9125-0.03940.1033-0.8229-0.0765-0.1639-0.774-0.05550.5592-0.00550.29910.07870.05640.40880.05680.3852-2.9753126.091-53.5987
103.66831.553-0.07213.0956-0.19481.64390.5093-0.5037-0.38480.6101-0.5189-0.03760.2578-0.04820.01720.549-0.0214-0.10010.39680.01210.2829-21.4634120.3406-42.9502
112.54751.9077-0.69891.943-0.46831.67970.1237-1.1621-0.24160.4005-0.3455-0.5165-0.07630.32050.07340.7255-0.1142-0.02250.36850.03620.4149-9.5287131.2335-40.8678
124.76722.60711.20613.4704-1.70213.0233-0.7728-0.8173-0.1161.5011-0.27710.88630.3723-1.14840.03780.7643-0.030.22020.7292-0.03710.329-26.2703125.219-37.472
132.60480.8166-1.41884.9802-0.59192.8279-0.4034-1.14220.20660.8029-0.4489-0.02750.92680.49770.29610.4212-0.0645-0.07990.5244-0.10330.34-12.8312124.9337-40.5329
143.12062.0697-0.22116.9465-1.30583.2044-0.3183-0.2372-0.01230.5855-0.5195-1.10020.27880.84070.2170.59950.0115-0.03850.61920.07110.3791-2.8769132.6916-47.9569
153.63371.49280.88054.8981-0.06433.60040.37970.1535-0.4622-0.6911-0.2413-0.09980.59230.287-0.04020.4394-0.02840.00710.31010.08510.2766-17.5697116.9808-49.1553
168.00850.58950.43246.3276-0.00264.01960.1518-0.0235-0.64470.0125-0.0708-0.07420.65680.2429-0.09740.4491-0.0437-0.05270.23120.02260.2818-21.7794115.6491-49.8141
174.10791.74691.50633.58310.46477.18260.811-0.1809-0.43550.7155-0.5456-0.06510.02151.77520.20440.6365-0.1669-0.24490.315-0.05550.5333-22.0943126.02756.7946
184.46420.08951.33044.1103-1.28087.2403-0.21390.6469-0.302-0.40930.1652-0.15150.6850.81380.07190.33170.0170.01890.3175-0.12650.3835-26.4994123.9353-15.2978
191.9990.67711.08021.895-0.92527.67880.21830.01830.20910.8274-0.137-0.356-0.30121.13240.07550.5879-0.089-0.17560.2689-0.00250.7014-23.566128.53533.4096
202.22221.7309-1.57283.7485-0.27413.39870.0758-1.42020.1191.4356-0.784-0.7698-0.4922-0.28780.12421.0055-0.1151-0.21030.6414-0.03590.5848-23.8487127.414319.2345
211.80350.48680.05162.7053-1.20684.3076-0.0695-0.10960.47110.8421-0.03230.1821-0.7107-0.4135-0.30260.48420.0262-0.0130.1651-0.01380.3392-37.4584127.6661.3462
220.73640.170.82621.2649-0.30863.3673-0.20.49790.9531-0.00310.15630.6348-0.5474-0.2415-0.03370.3559-0.0162-0.08810.27670.01910.6184-33.2403135.2284-7.7481
233.3487-1.0971-1.5145.1741.54858.463-0.64580.06770.96640.8968-0.0249-0.1844-0.9677-0.0716-0.56060.7296-0.11520.05290.36750.05480.6731-36.5976132.19959.767
242.8461-1.2319-1.2231.8974-0.22176.55190.4713-0.08770.87160.22610.2384-0.3-0.98450.1408-0.87030.5345-0.0227-0.08870.34980.00210.5581-29.0359132.987-3.8952
252.6658-0.56252.99173.406-0.71875.3976-0.32560.71390.2679-0.09050.3671-0.226-0.27940.59150.24230.3854-0.0854-0.0850.3356-0.00890.5122-31.947130.5812-16.3936
262.6621-0.03543.02743.5242-0.49153.48390.10420.1333-0.48960.152-0.4989-0.7212-0.28860.1680.03320.3808-0.02730.01220.3074-0.03950.2983-24.8964122.53732.5841
277.02730.11290.46414.4541-1.80546.98230.15580.3317-0.35330.4801-0.0165-0.50530.0045-0.00380.14570.6574-0.134-0.12340.21340.02370.2868-25.8636120.44026.4279
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 110 )
2X-RAY DIFFRACTION2chain 'A' and (resid 111 through 145 )
3X-RAY DIFFRACTION3chain 'A' and (resid 146 through 176 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 38 )
5X-RAY DIFFRACTION5chain 'B' and (resid 39 through 113 )
6X-RAY DIFFRACTION6chain 'B' and (resid 114 through 162 )
7X-RAY DIFFRACTION7chain 'B' and (resid 163 through 176 )
8X-RAY DIFFRACTION8chain 'C' and (resid 2 through 14 )
9X-RAY DIFFRACTION9chain 'C' and (resid 15 through 38 )
10X-RAY DIFFRACTION10chain 'C' and (resid 39 through 82 )
11X-RAY DIFFRACTION11chain 'C' and (resid 83 through 96 )
12X-RAY DIFFRACTION12chain 'C' and (resid 97 through 111 )
13X-RAY DIFFRACTION13chain 'C' and (resid 112 through 130 )
14X-RAY DIFFRACTION14chain 'C' and (resid 131 through 145 )
15X-RAY DIFFRACTION15chain 'C' and (resid 146 through 162 )
16X-RAY DIFFRACTION16chain 'C' and (resid 163 through 176 )
17X-RAY DIFFRACTION17chain 'D' and (resid 2 through 14 )
18X-RAY DIFFRACTION18chain 'D' and (resid 15 through 38 )
19X-RAY DIFFRACTION19chain 'D' and (resid 39 through 53 )
20X-RAY DIFFRACTION20chain 'D' and (resid 54 through 64 )
21X-RAY DIFFRACTION21chain 'D' and (resid 65 through 82 )
22X-RAY DIFFRACTION22chain 'D' and (resid 83 through 96 )
23X-RAY DIFFRACTION23chain 'D' and (resid 97 through 110 )
24X-RAY DIFFRACTION24chain 'D' and (resid 111 through 130 )
25X-RAY DIFFRACTION25chain 'D' and (resid 131 through 145 )
26X-RAY DIFFRACTION26chain 'D' and (resid 146 through 162 )
27X-RAY DIFFRACTION27chain 'D' and (resid 163 through 176 )

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