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- PDB-4f41: Protelomerase TelA mutant R255A complexed with CTTG hairpin DNA -

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Basic information

Entry
Database: PDB / ID: 4f41
TitleProtelomerase TelA mutant R255A complexed with CTTG hairpin DNA
Components
  • DNA hairpin
  • Protelomerase
KeywordsRECOMBINATION/DNA / RECOMBINATION-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
DNA / DNA (> 10) / Protelomerase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsShi, K. / Aihara, H.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Linear Chromosome-generating System of Agrobacterium tumefaciens C58: PROTELOMERASE GENERATES AND PROTECTS HAIRPIN ENDS.
Authors: Huang, W.M. / Dagloria, J. / Fox, H. / Ruan, Q. / Tillou, J. / Shi, K. / Aihara, H. / Aron, J. / Casjens, S.
History
DepositionMay 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protelomerase
C: DNA hairpin


Theoretical massNumber of molelcules
Total (without water)45,8982
Polymers45,8982
Non-polymers00
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-31 kcal/mol
Surface area19140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.322, 119.690, 58.724
Angle α, β, γ (deg.)90.00, 112.10, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protelomerase


Mass: 36070.121 Da / Num. of mol.: 1 / Fragment: UNP residues 102-421 / Mutation: R255A
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 hairpin


Mass: 9827.386 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 4.13 Å3/Da / Density % sol: 70.25 %
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: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 24, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 22125 / Num. obs: 22125 / % possible obs: 85.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.5→2.54 Å / % possible all: 34.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→37.77 Å / SU ML: 0.3 / σ(F): 0 / Phase error: 32.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.278 946 5.04 %
Rwork0.225 --
obs0.225 18780 72.3 %
all-18780 -
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.74 Å2 / ksol: 0.33 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.5253 Å2-0 Å23.2065 Å2
2---4.6631 Å2-0 Å2
3----15.5525 Å2
Refinement stepCycle: LAST / Resolution: 2.5→37.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2527 649 0 151 3327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033364
X-RAY DIFFRACTIONf_angle_d0.734698
X-RAY DIFFRACTIONf_dihedral_angle_d20.0571293
X-RAY DIFFRACTIONf_chiral_restr0.043516
X-RAY DIFFRACTIONf_plane_restr0.003486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.6330.3098220.3455476X-RAY DIFFRACTION13
2.633-2.79790.3922730.32391362X-RAY DIFFRACTION39
2.7979-3.01390.41961300.31952369X-RAY DIFFRACTION68
3.0139-3.3170.35191460.28953203X-RAY DIFFRACTION90
3.317-3.79660.28651950.22353429X-RAY DIFFRACTION98
3.7966-4.78180.22782000.17533457X-RAY DIFFRACTION98
4.7818-37.7670.22381800.19143538X-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)
12.9939-0.7170.52466.62832.36266.28660.29790.1285-0.26640.0515-0.0184-0.160.11050.3987-0.30580.26560.05950.09720.2624-0.03130.910833.7106-30.59190.9495
21.0346-0.6498-0.13081.6168-0.05370.61-0.1931-0.1223-0.63620.28960.0023-0.34450.13120.0429-0.20.14380.1526-0.0636-0.09770.11530.72121.2122-33.016.1334
31.22080.04250.37451.7974-0.04631.58380.1119-0.1731-0.1970.26770.08040.07040.06820.11920.37690.06050.0772-0.00990.18220.1146-0.02374.7635-14.193910.2301
41.117-0.67030.26211.0960.22610.2463-0.14570.33880.919-0.19560.0599-0.9095-0.26890.5529-0.0533-0.4244-0.55260.2203-1.0140.18370.130820.22270.7177-2.9561
5-0.00010.0002-0.00030.0086-0.01280.02090.048-0.16570.37570.2155-0.27370.9976-0.1015-0.35870.22030.2421-0.00030.05860.2522-0.24150.91271.74715.10698.3349
60.11370.57630.47056.10522.36271.94780.02530.02340.0132-0.52370.0326-0.38840.11580.21920.00390.27470.01130.04290.4306-0.21950.309510.133-15.2961-4.876
71.26430.37510.56552.05651.44071.086-0.1769-0.0228-0.13410.03080.05490.06460.2712-0.02620.17020.50810.08410.08440.4079-0.22460.35276.7043-18.3034-5.6429
81.70231.04321.63166.4336-4.75217.2734-0.11410.01580.17960.16290.16760.0999-0.1593-0.1608-0.04690.3877-0.1052-0.1230.49940.07441.30683.0373-21.6795-3.2221
90.4933-0.3103-0.61381.8941.08291.04950.1913-0.4177-0.38410.1348-0.23850.19270.1661-0.30530.01720.3755-0.1216-0.11110.95980.50890.86526.0179-24.04470.5033
103.1253-2.9368-0.52943.66420.93792.43170.17230.0327-0.360.1524-0.38130.64420.4558-0.36290.21630.4411-0.1794-0.18320.3842-0.05240.542110.7073-23.89891.609
111.27751.37211.30043.4799-0.28342.7310.23690.1040.0447-0.4419-0.10510.0725-0.1481-0.1592-0.04870.22670.01020.04070.1140.02140.458615.2909-21.76730.3725
125.03951.36390.45974.3224-2.92595.67190.02630.007-0.0401-0.0458-0.05350.02040.0077-0.05230.04010.2422-0.0521-0.04360.1941-0.110.156818.5973-17.9013-0.4718
132.2154-1.12162.18990.7581-0.78252.7227-0.045-0.20730.1121-0.03560.11340.10620.0068-0.2724-0.06670.1427-0.0492-0.13340.32860.05590.57120.9075-14.02180.479
140.0031-0.0028-0.02410.11-0.00890.19820.032-0.10850.0299-0.0012-0.00680.00740.0217-0.0520.03130.1629-0.0567-0.19940.2291-0.05750.488321.871-10.34434.2336
151.9999-1.2831-1.87390.7398-0.51223.48960.03030.0109-0.63970.0330.0390.2640.08580.1794-0.07530.1692-0.04170.04760.3097-0.25550.629622.4802-9.66369.7323
165.25724.6507-0.30634.88860.81381.53690.14010.1628-0.54440.09780.03-0.34840.21810.1742-0.15860.3246-0.0386-0.25340.4706-0.07070.769623.969-9.860414.3219
177.23130.2627-6.32273.21670.81148.0530.0782-0.0502-0.5228-0.26360.3037-0.13671.14840.5733-0.34750.75990.1071-0.29670.6795-0.13870.384326.256-12.139818.5073
184.6322-0.3346-4.48932.63332.23195.97830.0602-0.72-0.33540.1290.18070.13020.3916-0.4473-0.22910.62750.1433-0.39841.09510.04590.806829.0196-16.013821.1866
196.51534.6419-3.87113.637-2.4172.65270.1485-0.7097-0.92320.0826-0.0443-0.22070.55040.5124-0.14310.73580.1215-0.50710.98090.13191.194232.5617-19.315621.7857
209.18015.3193-5.14476.2203-1.21163.8809-0.2021-0.21180.2296-0.37970.35921.02340.6391-0.4851-0.16110.73950.1677-0.47161.21180.0471.359937.3625-20.836920.4003
216.7323-1.55251.61028.05892.07935.27450.01860.1005-0.23550.03120.2725-0.31470.17930.2031-0.37230.5834-0.1172-0.44091.1699-0.08010.916842.5429-20.503319.7163
220.26040.28110.39213.05193.62784.7038-0.0267-0.220.05780.24290.308-0.72550.06871.0611-0.29320.655-0.0912-0.47491.38730.14041.431646.6157-18.713419.9808
233.43531.204-5.04461.1391-1.91927.4399-0.45630.8661-0.8311-0.1345-0.1492-0.06551.0805-0.70170.57320.8333-0.4639-0.14751.7592-0.3091.486849.4392-15.023621.4914
240.4007-0.68110.31451.1578-0.53460.2468-0.4841-0.50060.8155-0.29980.13860.7753-1.0696-0.32370.36831.3429-0.158-0.63431.2422-0.4261.465243.8396-12.52430.3904
254.7157-3.2408-3.46659.30096.81345.32410.4031-2.20731.76052.90760.1857-2.1732-0.49230.7982-0.55391.43360.163-0.41911.7887-0.11211.546442.6325-10.575527.4259
265.17983.7289-2.7914.3239-1.9461.50630.1049-0.88131.30420.5136-0.1269-0.1995-1.12020.43390.03380.9691-0.053-0.40561.3344-0.0711.408740.8206-8.632123.5714
275.69224.5989-3.28072-4.170321.0816-2.04710.46151.8393-1.24580.1416-0.41550.46560.17251.0054-0.1889-0.5741.1028-0.06561.307540.1665-9.792918.1135
289.5883-2.7322-3.54031.6962-0.17032.8218-0.0972-0.44761.09320.1542-0.0925-0.0777-0.51180.78910.20270.7922-0.0884-0.55560.6674-0.05331.146139.2059-12.449314.3543
294.0747-2.53562.60252.44840.03495.4478-0.0659-0.2928-0.16820.0854-0.1286-0.49620.04930.70.17060.41560.0366-0.28150.85080.11021.073536.6974-15.907312.0361
306.72194.40812.43615.03630.34372.45580.22490.7559-1.11730.08530.3776-1.02220.55850.5662-0.64880.34750.0977-0.25880.4045-0.2390.930732.652-18.820511.1907
317.9958-0.43657.27936.6215-1.92977.7653-0.18640.27230.73050.06170.1768-0.0173-0.3517-0.495-0.02240.21780.0118-0.10640.54570.13780.703328.1985-20.670313.1698
329.31028.2926-2.47627.9543-2.68676.27090.2072-0.5099-0.52890.1025-0.2136-0.14680.08910.5573-0.02250.14740.0046-0.01180.5629-0.14080.571224.1391-20.249915.2664
333.2941.9341-1.07076.7749-7.36469.80290.2687-0.7385-0.28820.7461-0.09980.0293-0.3012-0.2165-0.12180.319-0.1077-0.12120.3707-0.00510.289920.027-17.293114.0615
343.7606-2.4318-3.4563.00462.69983.369-0.1257-0.4957-0.26990.16170.32890.10050.26790.103-0.15540.3230.104-0.22590.32510.04080.457516.5514-14.482711.9032
355.40654.4665-0.38084.2137-0.62732.75270.0602-0.0298-0.2160.00210.118-0.15250.0979-0.1372-0.05350.2288-0.1143-0.04790.29730.14430.346114.0773-11.88658.537
362.04460.92020.1324.88481.96691.33160.1012-0.0703-0.00360.3576-0.0705-0.08420.22420.0002-0.00780.39210.0613-0.16330.3394-0.11420.242912.6938-10.86133.6116
372.21481.4455-0.90583.1821-2.94384.15310.0931-0.39990.05720.2255-0.14730.15690.13910.1940.01470.3027-0.01740.04270.1583-0.04190.07111.2752-13.1276-1.0392
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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