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- PDB-4e0g: Protelomerase tela/DNA hairpin product/vanadate complex -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4e0g
TitleProtelomerase tela/DNA hairpin product/vanadate complex
Components
  • DNA (5'-D(*CP*AP*TP*AP*AP*TP*AP*AP*CP*AP*AP*TP*A)-3')
  • DNA (5'-D(*TP*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 PAIRPIN / DNA HAIRPIN / 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 / hpI Integrase; Chain A / Helix Hairpins / Helix non-globular / Special / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
VANADATE ION / DNA / DNA (> 10) / Protelomerase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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*A)-3')
D: DNA (5'-D(*TP*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)62,4754
Polymers62,3603
Non-polymers1151
Water7,296405
1
A: Protelomerase
C: DNA (5'-D(*CP*AP*TP*AP*AP*TP*AP*AP*CP*AP*AP*TP*A)-3')
D: DNA (5'-D(*TP*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*A)-3')
D: DNA (5'-D(*TP*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)124,9498
Polymers124,7196
Non-polymers2302
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area16300 Å2
ΔGint-82 kcal/mol
Surface area35280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.880, 120.200, 58.040
Angle α, β, γ (deg.)90.00, 111.85, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protelomerase / Telomere resolvase


Mass: 52568.188 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
#2: DNA chain DNA (5'-D(*CP*AP*TP*AP*AP*TP*AP*AP*CP*AP*AP*TP*A)-3')


Mass: 3951.639 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*TP*CP*AP*TP*GP*AP*TP*AP*TP*TP*GP*TP*TP*AP*TP*TP*AP*TP*G)-3')


Mass: 5839.804 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-VO4 / VANADATE ION / Vanadate


Mass: 114.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: VO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 3.06 Å3/Da / Density % sol: 59.8 %
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: 1.99→50 Å / Num. all: 51367 / Num. obs: 51367 / % possible obs: 82 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.99→2.03 Å / % possible all: 69.2

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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: 2.2→40.115 Å / SU ML: 0.22 / σ(F): 0 / Phase error: 24.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.238 1567 5.17 %
Rwork0.1939 --
obs0.1962 30327 79.65 %
all-30329 -
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.039 Å2 / ksol: 0.364 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.56 Å20 Å21.7236 Å2
2--3.5032 Å2-0 Å2
3----11.6775 Å2
Refinement stepCycle: LAST / Resolution: 2.2→40.115 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2533 650 3 405 3591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083427
X-RAY DIFFRACTIONf_angle_d1.0844790
X-RAY DIFFRACTIONf_dihedral_angle_d20.4531341
X-RAY DIFFRACTIONf_chiral_restr0.072524
X-RAY DIFFRACTIONf_plane_restr0.004498
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2710.2506850.2011506X-RAY DIFFRACTION46
2.271-2.35220.25151120.21291708X-RAY DIFFRACTION53
2.3522-2.44630.29351050.22671957X-RAY DIFFRACTION60
2.4463-2.55770.2871180.23782274X-RAY DIFFRACTION69
2.5577-2.69250.2971390.2462499X-RAY DIFFRACTION77
2.6925-2.86110.34021580.24782847X-RAY DIFFRACTION87
2.8611-3.0820.29471630.24343207X-RAY DIFFRACTION97
3.082-3.3920.26651770.20973220X-RAY DIFFRACTION98
3.392-3.88240.22911840.17263220X-RAY DIFFRACTION98
3.8824-4.89010.16791680.13343170X-RAY DIFFRACTION97
4.8901-40.12120.1611580.16883152X-RAY DIFFRACTION94
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)
17.3786-1.3631.56636.76611.61175.0618-0.08830.14520.10510.1780.0885-0.6288-0.0910.285-0.02420.23290.06120.02030.2745-0.01191.047633.8361-30.64470.9608
21.314-0.6028-0.07872.1783-0.01420.8128-0.1727-0.1524-0.49270.2544-0.0632-0.20220.19040.08570.06950.15280.1347-0.15110.02830.10830.818121.1489-33.18236.0104
30.3728-1.382-0.0798.5217-0.32340.4464-0.0231-0.1933-0.20330.39060.00730.13510.11210.02020.02140.21740.04950.04570.2353-0.0539-0.00134.7153-14.23049.9777
41.5309-0.55610.07711.2990.17430.4746-0.00880.15250.9128-0.1171-0.0101-1.0361-0.13260.0549-0.01840.0898-0.16320.1026-0.06330.070.537920.31570.6273-2.7401
56.4568-6.031-3.20685.63172.99561.59180.12650.3402-0.38760.0367-0.49881.6153-0.2727-0.89240.38480.5273-0.03910.10180.4488-0.30350.93511.645814.88018.042
63.35023.0582-4.39216.7374-5.36056.997-0.02130.05460.0268-0.22740.1413-0.42410.18880.0251-0.11190.2032-0.0692-0.02440.174-0.10680.405510.2469-15.3864-4.9882
72.00011.9821-4.27435.82360.3968.7702-0.0542-0.24720.74-0.04-0.07930.2605-0.3606-0.26640.1210.2647-0.089-0.16250.3088-0.15520.45516.6776-18.4351-5.3258
81.87033.9567-1.05238.3738-2.12243.4188-0.0402-0.1007-0.63230.108-0.08470.30610.054-0.13320.11830.2665-0.1104-0.11410.3580.01130.75383.0842-21.4147-3.1219
92.11120.32250.76160.04890.1160.27420.3654-0.6816-1.1340.2411-0.008-0.01010.6452-0.2844-0.37950.2222-0.0775-0.23850.44960.18580.55525.9905-23.97960.2881
107.35011.9998-5.02011.99992.00017.38420.13630.0172-0.83420.2293-0.11620.98081.1358-0.6354-0.01870.2674-0.1147-0.11910.19960.06520.166110.5902-23.88481.5181
115.31492.4541-4.06022-6.87142.00010.00010.0358-0.1112-0.3283-0.14310.1737-0.0057-0.12450.13820.10760.0266-0.05940.0774-0.0660.313415.2986-21.86260.4445
120.7719-2.40270.12897.4781-0.40120.02160.05750.2316-0.1089-0.62960.1314-0.3046-0.11050.0886-0.19730.1572-0.0906-0.03980.1154-0.08130.233818.6616-17.9241-0.4578
132.47511.171-1.69360.6244-0.53662.150.1132-0.32-0.24420.0646-0.18710.00040.1706-0.05960.07130.092-0.0504-0.09070.25370.00150.37121.0698-14.05570.3741
147.1087-1.05580.32553.79874.57168.84640.04210.1085-0.0571-0.06210.0616-0.06870.00710.057-0.08970.1704-0.0397-0.23710.15010.00130.457122.0845-10.46864.1798
153.70611.2876-1.62790.79790.19262.3546-0.0556-0.05440.10520.14040.03170.3813-0.192-0.14590.02990.1886-0.1346-0.18660.3056-0.09740.348222.5067-9.71489.7014
163.93593.4170.84153.45652.77488.7062-0.2119-0.05080.5124-0.0292-0.15570.3956-0.3811-0.4610.37510.3066-0.0116-0.25160.4608-0.09870.429324.1047-10.005614.34
176.6275-3.0399-1.77238.65123.35817.4103-0.0284-0.35150.0590.0768-0.05240.3172-0.0064-0.69140.08850.4187-0.0629-0.34180.6641-0.02980.46426.4303-12.219218.4634
187.90953.2285-2.85159.4706-2.04328.37520.0244-0.9276-0.36730.1930.11760.46930.3882-1.033-0.14860.4892-0.0179-0.47690.56620.06730.547229.1716-16.23821.1211
196.52227.7221-2.8029.1452-3.47161.99980.404-0.3466-1.27690.0448-0.212-0.03030.82890.2244-0.19830.54490.184-0.43360.93970.16590.89432.7391-19.375121.8163
202.0001-9.7708-1.39057.0289-0.14121.99990.6398-0.145-1.7782-0.3529-0.16891.09090.8459-0.9007-0.48090.47420.1004-0.37940.86530.07730.986437.4762-20.916720.7013
214.60481.96985.50981.99996.92048.08560.4140.2709-1.0633-0.0020.0098-0.2660.54080.6152-0.44140.53720.0265-0.51130.8821-0.02671.090942.4807-20.5919.9254
226.5829-7.0558-4.85088.9117.34377.58950.57980.6857-1.11590.06360.013-1.05930.62050.7535-0.59810.6210.0549-0.54081.0271-0.14911.249346.7948-18.60419.8199
237.1843-1.3661-8.98380.25931.70841.99990.17212.0417-0.6589-0.71790.43970.15860.74310.8174-0.61510.8999-0.1123-0.7251.16070.0011.252752.1433-15.513122.4558
249.4845-1.18482.00013.84394.17172-1.6065-0.97754.07380.33250.19020.6199-2.9971-1.42911.42440.90950.1623-0.66720.9005-0.07461.300347.2645-12.483831.2321
2523.59171.20591.99996.06237.4595-0.7867-2.18042.41441.5505-0.1574-0.832-1.2766-0.0330.95450.93250.1309-0.75511.1241-0.12161.281742.8476-11.194527.792
2624.5035-4.86649.9103-9.61769.3631-1.1742-1.55713.81491.1881-0.5397-0.5553-2.92931.30461.72621.04040.0247-0.75771.0751-0.10511.41340.9644-9.460423.5076
27222.00011.99991.99981.9999-0.1011-2.64572.80192.1708-1.403-1.2246-2.60391.31191.51040.9197-0.1053-0.64650.8520.11861.123640.4669-10.152617.9514
282-9.4342-5.17025.83191.95951.9999-0.6410.99363.41480.07550.1519-0.8914-1.31511.61180.4970.4757-0.0424-0.43530.6070.05820.956139.1633-12.586714.4098
2921.9999-0.76318.84882.93819.67690.04340.58750.33090.23430.196-1.11930.00530.7271-0.24730.3777-0.0909-0.39520.48830.0490.906336.7189-16.042512.1149
306.52494.65483.7597.54420.11624.43460.3340.4962-0.77020.22180.1199-1.18910.57880.4141-0.46130.27040.0456-0.35460.3786-0.05340.715832.7251-18.942311.2425
317.45252.18063.91153.9831-0.66435.77390.12310.1513-0.37470.0248-0.0702-0.04790.17470.1889-0.05710.186-0.0178-0.24950.38450.08940.579628.3046-20.834913.0256
320.7162-1.31731.25312.4466-2.43082.86140.2117-0.7581-1.080.060.1980.12270.71630.2023-0.41490.2510.0506-0.26530.40030.03520.64324.2509-20.32115.1439
3324.5251-1.79743.33593.44762.00010.1972-0.3476-0.32060.2036-0.0498-0.1520.33430.3198-0.14340.259-0.0576-0.20810.37040.0090.391520.0925-17.381713.9206
343.3126-1.5999-0.41352.33721.09120.5592-0.0252-0.3845-0.08040.19030.1302-0.05070.1810.0268-0.10090.19410.0267-0.20760.40.02230.332516.5914-14.571411.79
354.48542.41784.04119.60974.38314.2257-0.0708-0.0580.11690.05140.0337-0.00590.0182-0.06120.03690.17850.0327-0.1880.1515-0.10360.433514.1713-11.87678.4306
364.90921.34440.69892.0001-2.07681.88520.0051-0.40910.39810.3088-0.06880.1998-0.2901-0.03810.04810.17770.0096-0.00780.131-0.05840.044612.847-10.80663.4657
370.4835-0.2861-0.49830.16910.29480.5132-0.08740.0673-0.0794-0.11660.0355-0.07550.0864-0.02790.05820.1521-0.0962-0.02680.1166-0.0310.254411.3843-13.2846-1.0332
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 103:122
2X-RAY DIFFRACTION2chain A and resid 124:195
3X-RAY DIFFRACTION3chain A and resid 197:219
4X-RAY DIFFRACTION4chain A and resid 220:409
5X-RAY DIFFRACTION5chain A and resid 410:421
6X-RAY DIFFRACTION6chain C and resid 15:15
7X-RAY DIFFRACTION7chain C and resid 16:16
8X-RAY DIFFRACTION8chain C and resid 17:17
9X-RAY DIFFRACTION9chain C and resid 18:18
10X-RAY DIFFRACTION10chain C and resid 19:19
11X-RAY DIFFRACTION11chain C and resid 20:20
12X-RAY DIFFRACTION12chain C and resid 21:21
13X-RAY DIFFRACTION13chain C and resid 22:22
14X-RAY DIFFRACTION14chain C and resid 23:23
15X-RAY DIFFRACTION15chain C and resid 24:24
16X-RAY DIFFRACTION16chain C and resid 25:25
17X-RAY DIFFRACTION17chain C and resid 26:26
18X-RAY DIFFRACTION18chain C and resid 27:27
19X-RAY DIFFRACTION19chain C and resid 28:28
20X-RAY DIFFRACTION20chain C and resid 29:29
21X-RAY DIFFRACTION21chain C and resid 30:30
22X-RAY DIFFRACTION22chain C and resid 31:31
23X-RAY DIFFRACTION23chain C and resid 32:32
24X-RAY DIFFRACTION24chain C and resid 1:1
25X-RAY DIFFRACTION25chain C and resid 2:2
26X-RAY DIFFRACTION26chain C and resid 3:3
27X-RAY DIFFRACTION27chain C and resid 4:4
28X-RAY DIFFRACTION28chain C and resid 5:5
29X-RAY DIFFRACTION29chain C and resid 6:6
30X-RAY DIFFRACTION30chain C and resid 7:7
31X-RAY DIFFRACTION31chain C and resid 8:8
32X-RAY DIFFRACTION32chain C and resid 9:9
33X-RAY DIFFRACTION33chain C and resid 10:10
34X-RAY DIFFRACTION34chain C and resid 11:11
35X-RAY DIFFRACTION35chain C and resid 12:12
36X-RAY DIFFRACTION36chain C and resid 13:13
37X-RAY DIFFRACTION37chain C and resid 14:14

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