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- PDB-4e0y: Protelomerase tela covalently complexed with mutated substrate DNA -

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Basic information

Entry
Database: PDB / ID: 4e0y
TitleProtelomerase tela covalently complexed with mutated substrate DNA
Components
  • DNA (5'-D(*CP*AP*TP*AP*AP*TP*AP*AP*CP*AP*AP*TP*AP*T)-3')
  • DNA (5'-D(*CP*CP*AP*TP*GP*AP*TP*AP*TP*TP*GP*TP*TP*AP*TP*TP*AP*TP*G)-3')
  • ProtelomeraseTelomere resolvase
KeywordsDNA BINDING PROTEIN/DNA / PROTELEMORASE / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


Helix Hairpins - #1780 / Telomere resolvase / Telomere resolvase ResT / Telomere resolvase ResT superfamily / Telomere resolvase ResT/TelK catalytic domain / hpI Integrase; Chain A / Helix Hairpins / Helix non-globular / Special / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
THYMIDINE-5'-MONOPHOSPHATE / DNA / DNA (> 10) / Protelomerase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsShi, K. / Aihara, H.
CitationJournal: Plos Biol. / Year: 2013
Title: An enzyme-catalyzed multistep DNA refolding mechanism in hairpin telomere formation.
Authors: Shi, K. / Huang, W.M. / Aihara, H.
History
DepositionMar 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protelomerase
C: DNA (5'-D(*CP*AP*TP*AP*AP*TP*AP*AP*CP*AP*AP*TP*AP*T)-3')
D: DNA (5'-D(*CP*CP*AP*TP*GP*AP*TP*AP*TP*TP*GP*TP*TP*AP*TP*TP*AP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1435
Polymers62,7293
Non-polymers4142
Water2,450136
1
A: Protelomerase
C: DNA (5'-D(*CP*AP*TP*AP*AP*TP*AP*AP*CP*AP*AP*TP*AP*T)-3')
D: DNA (5'-D(*CP*CP*AP*TP*GP*AP*TP*AP*TP*TP*GP*TP*TP*AP*TP*TP*AP*TP*G)-3')
hetero molecules

A: Protelomerase
C: DNA (5'-D(*CP*AP*TP*AP*AP*TP*AP*AP*CP*AP*AP*TP*AP*T)-3')
D: DNA (5'-D(*CP*CP*AP*TP*GP*AP*TP*AP*TP*TP*GP*TP*TP*AP*TP*TP*AP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,28610
Polymers125,4586
Non-polymers8294
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area15190 Å2
ΔGint-70 kcal/mol
Surface area35310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.984, 119.442, 56.922
Angle α, β, γ (deg.)90.00, 112.42, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Protelomerase / Telomere resolvase


Mass: 52648.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: C58 / ATCC 33970 / Gene: telA, Atu2523 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7CWV1

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA (5'-D(*CP*AP*TP*AP*AP*TP*AP*AP*CP*AP*AP*TP*AP*T)-3')


Mass: 4255.832 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*CP*CP*AP*TP*GP*AP*TP*AP*TP*TP*GP*TP*TP*AP*TP*TP*AP*TP*G)-3')


Mass: 5824.793 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 138 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-DT / THYMIDINE-5'-MONOPHOSPHATE / Thymidine monophosphate


Type: DNA linking / Mass: 322.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O8P / Comment: dTMP*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.93 Å3/Da / Density % sol: 58.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 5% (w/v) PEG 4000, 10mM Tris-HCl, 300mM NaCl , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 96 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 21996 / Num. obs: 21996 / % possible obs: 77.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→40.082 Å / SU ML: 0.28 / σ(F): 0 / Phase error: 33.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2698 1120 5.1 %
Rwork0.2159 --
obs0.2187 21975 77.69 %
all-21975 -
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.388 Å2 / ksol: 0.335 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.3904 Å2-0 Å22.9442 Å2
2--3.9598 Å20 Å2
3----7.3502 Å2
Refinement stepCycle: LAST / Resolution: 2.4→40.082 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2528 593 23 136 3280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033315
X-RAY DIFFRACTIONf_angle_d0.8574616
X-RAY DIFFRACTIONf_dihedral_angle_d19.6321284
X-RAY DIFFRACTIONf_chiral_restr0.05505
X-RAY DIFFRACTIONf_plane_restr0.003490
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.50920.3671730.27421301X-RAY DIFFRACTION39
2.5092-2.64150.3303760.27261730X-RAY DIFFRACTION51
2.6415-2.8070.34551030.29392160X-RAY DIFFRACTION64
2.807-3.02360.32251620.30182627X-RAY DIFFRACTION79
3.0236-3.32780.32121740.25683123X-RAY DIFFRACTION94
3.3278-3.8090.29641950.20853308X-RAY DIFFRACTION98
3.809-4.79770.21651690.16773278X-RAY DIFFRACTION98
4.7977-40.0880.2191680.19183328X-RAY DIFFRACTION97
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)
18.9326-2.21882.43382.7925-0.05763.3695-0.03250.4256-0.2185-0.0370.06030.03810.1080.3099-0.04120.26140.06880.01440.4632-0.00311.263231.1659-32.2713-1.4324
21.41763.0312.04386.4824.32224.6697-0.19060.0919-1.1605-0.06560.5967-2.30420.28721.4831-0.41360.6152-0.0325-0.23620.8544-0.08271.742542.8244-23.2169.501
35.6454-4.14833.26046.3551.65166.8339-0.0933-0.10110.0440.71730.3508-0.61660.17380.342-0.20780.43760.0781-0.26930.38710.14251.034331.7041-26.750112.4621
43.9884-0.9956-0.22035.65350.70380.94510.06210.0741-0.65050.0323-0.02950.16530.1058-0.1241-0.11360.26060.0806-0.15740.18580.00011.114623.0768-41.08632.6544
52.4701-3.4163-0.63095.90761.81514.0437-0.2885-0.1451-0.19111.00660.4254-0.12390.0647-0.0059-0.1240.44980.034-0.02850.30210.15261.239817.7896-37.60499.7406
63.8675-0.61771.7088.30814.99414.1336-0.4053-1.2498-0.82581.46710.3531-0.05931.07020.40730.03680.53430.0569-0.1890.42270.27370.819516.0767-24.335615.2743
70.51640.0244-0.09425.16820.45513.58260.019-0.06930.41240.47260.1477-1.266-0.34740.3269-0.14270.33220.0543-0.05490.1109-0.00230.637918.901-24.91256.6772
80.52340.0114-0.14656.51750.94581.42240.10970.0958-0.2366-0.5270.02730.11050.0169-0.0623-0.0440.2874-0.0262-0.15640.1459-0.04631.109318.5995-33.7819-2.0425
98.5149-6.5324-0.61275.08571.09685.3413-0.1275-0.3543-1.19770.034-0.22711.43240.1553-0.51620.38050.2704-0.0449-0.10420.34480.00930.4144.7582-20.09139.2244
102.3719-2.2232-0.78623.63330.44461.18020.1519-0.2550.89820.0490.0458-1.2726-0.20120.05250.06990.2776-0.1130.03270.10570.05970.391821.00433.91182.9131
113.3593-1.44481.58777.2384-5.21067.11810.03580.60620.6289-0.62720.24640.2685-0.3621-0.1595-0.52080.5935-0.13470.24160.54580.30921.022621.78242.3373-16.3461
120.453-0.32040.02041.9024-0.98841.9659-0.12850.34640.1575-0.20710.0395-0.0703-0.1966-0.092-0.20910.4710.01410.13460.58250.20570.172819.09742.0735-12.3851
132.22242.020.09942.0837-0.21262.08710.7341.7735-1.7124-1.6726-0.0690.54041.1918-0.3525-0.66571.0555-0.138-0.00260.7732-0.19070.639313.3149-16.5641-13.248
142.79440.1983-0.20160.16280.69323.3686-0.19680.4050.3506-0.43380.0054-0.4141-0.36330.3941-0.02010.3549-0.02960.18860.37620.25110.502620.18132.475-11.6347
151.2551-0.57950.40532.7462-0.00961.5469-0.10570.1330.3956-0.1729-0.1157-1.13720.11070.37560.2060.33040.0575-0.05230.23870.02541.293432.9522-6.5005-1.8835
168.80532.0674-6.0262.4539-0.78856.7043-0.1592-1.27050.74740.70370.1714-0.8072-0.20760.6756-0.01020.38130.0505-0.30920.3395-0.09630.796622.2163.643413.2501
173.04852.0233-0.38733.87661.71541.58720.03170.1620.7708-0.03820.0326-0.1366-0.106-0.15920.02590.2308-0.0056-0.0805-0.00430.09150.48859.52762.6112-3.6146
183.6994-2.26711.34564.082.87335.57-0.0460.9948-0.3866-1.0175-0.0947-0.31510.77020.10620.16240.5159-0.05390.01740.32620.02190.33064.1493-9.8191-6.6719
194.8135-0.55010.85415.98672.9084.48830.0877-0.36840.9985-0.0199-0.1998-0.1051-0.27060.040.12430.2111-0.0280.09910.2998-0.09130.34837.5072.98484.8404
207.04810.9393-0.23260.1826-0.36962.00420.3495-0.1691.9483-0.4522-0.01780.2812-1.0776-0.0427-0.32310.8971-0.0366-0.14750.3148-0.16261.1353-1.931216.33289.5505
214.6612-2.52873.19381.9723-3.0525.3066-0.7496-1.03251.27350.6302-0.1718-0.3203-1.3331-0.6551.0791.01250.106-0.75011.1335-0.19991.443742.1107-11.053424.4685
222.699-0.34642.65221.3980.0022.83620.0075-0.08-0.2340.10670.0843-0.40540.090.5803-0.17880.2557-0.0087-0.32430.420.03091.03427.8499-17.399512.9199
232.60572.7305-0.18982.8661-0.27381.20830.0069-0.12230.0767-0.04090.1936-0.2431-0.0570.2071-0.15420.1741-0.0466-0.04290.43170.01040.735913.9455-11.90818.4918
246.73186.8822-0.09847.6496-0.07710.00240.1019-0.19670.44740.43470.0121-0.1547-0.01030.0192-0.08040.34050.0576-0.17930.2544-0.06240.680912.6504-10.90843.604
253.58331.5125-3.71241.6258-2.2244.5738-0.1980.5359-0.8225-0.4159-0.0478-0.48350.76340.010.23491.47560.2669-0.41261.60630.05131.40852.0845-22.6263-3.9665
262.46850.55-0.92053.8038-4.37545.29190.1521.637-1.707-1.23480.11171.85931.2476-2.4062-0.25510.4649-0.0867-0.21070.8038-0.12520.92539.4855-24.9207-0.6044
271.05031.09660.64392.74640.01320.6645-0.0984-0.04820.0156-0.0221-0.0258-0.3687-0.04140.04150.04110.23770.0213-0.18330.2198-0.04180.955520.8009-13.07583.6594
287.2706-2.10410.08566.2182-1.66977.03710.0898-0.6612-0.82310.33950.07330.11980.53310.241-0.1680.5735-0.0255-0.42310.420.04841.038327.6308-14.866118.8802
293.96690.23625.02963.77382.55417.72670.10210.8695-0.68590.11980.1056-0.36970.10890.7925-0.41830.61430.009-0.57331.08720.01451.412144.3898-19.237920.1863
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 102:118)
2X-RAY DIFFRACTION2(chain A and resid 119:123)
3X-RAY DIFFRACTION3(chain A and resid 124:133)
4X-RAY DIFFRACTION4(chain A and resid 134:148)
5X-RAY DIFFRACTION5(chain A and resid 149:161)
6X-RAY DIFFRACTION6(chain A and resid 162:169)
7X-RAY DIFFRACTION7(chain A and resid 170:175)
8X-RAY DIFFRACTION8(chain A and resid 176:195)
9X-RAY DIFFRACTION9(chain A and resid 196:210)
10X-RAY DIFFRACTION10(chain A and resid 211:260)
11X-RAY DIFFRACTION11(chain A and resid 261:272)
12X-RAY DIFFRACTION12(chain A and resid 273:286)
13X-RAY DIFFRACTION13(chain A and resid 287:292)
14X-RAY DIFFRACTION14(chain A and resid 293:313)
15X-RAY DIFFRACTION15(chain A and resid 314:343)
16X-RAY DIFFRACTION16(chain A and resid 344:361)
17X-RAY DIFFRACTION17(chain A and resid 362:394)
18X-RAY DIFFRACTION18(chain A and resid 395:400)
19X-RAY DIFFRACTION19(chain A and resid 401:414)
20X-RAY DIFFRACTION20(chain A and resid 415:421)
21X-RAY DIFFRACTION21(chain C and resid 1:4)
22X-RAY DIFFRACTION22(chain C and resid 5:11)
23X-RAY DIFFRACTION23(chain C and resid 12:12)
24X-RAY DIFFRACTION24(chain C and resid 13:13)
25X-RAY DIFFRACTION25(chain C and resid 17:17)
26X-RAY DIFFRACTION26(chain C and resid 18:20)
27X-RAY DIFFRACTION27(chain C and resid 21:24)
28X-RAY DIFFRACTION28(chain C and resid 25:28)
29X-RAY DIFFRACTION29(chain C and resid 29:32)

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