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- PDB-1l6b: CRYSTAL STRUCTURE ANALYSIS OF THE ALL DNA HOLLIDAY JUNCTION STRUC... -

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Basic information

Entry
Database: PDB / ID: 1l6b
TitleCRYSTAL STRUCTURE ANALYSIS OF THE ALL DNA HOLLIDAY JUNCTION STRUCTURE OF CCGGTACM5CGG
Components5'-D(*CP*CP*GP*GP*TP*AP*CP*(5CM)P*GP*G)-3'
KeywordsDNA / Holliday Junction / DNA four-way junction / cytosine methylation
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsVargason, J.M. / Ho, P.S.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: The effect of cytosine methylation on the structure and geometry of the Holliday junction: the structure of d(CCGGTACm5CGG) at 1.5 A resolution.
Authors: Vargason, J.M. / Ho, P.S.
History
DepositionMar 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _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: 5'-D(*CP*CP*GP*GP*TP*AP*CP*(5CM)P*GP*G)-3'
B: 5'-D(*CP*CP*GP*GP*TP*AP*CP*(5CM)P*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1603
Polymers6,1202
Non-polymers401
Water1,71195
1
A: 5'-D(*CP*CP*GP*GP*TP*AP*CP*(5CM)P*GP*G)-3'
B: 5'-D(*CP*CP*GP*GP*TP*AP*CP*(5CM)P*GP*G)-3'
hetero molecules

A: 5'-D(*CP*CP*GP*GP*TP*AP*CP*(5CM)P*GP*G)-3'
B: 5'-D(*CP*CP*GP*GP*TP*AP*CP*(5CM)P*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3206
Polymers12,2404
Non-polymers802
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)65.503, 24.704, 36.975
Angle α, β, γ (deg.)90.00, 110.01, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-108-

HOH

21B-76-

HOH

DetailsThe second part of the biological assembly is generated by a crystallographic two-fold to give one fully watson-crick basepaired Holliday junction

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Components

#1: DNA chain 5'-D(*CP*CP*GP*GP*TP*AP*CP*(5CM)P*GP*G)-3'


Mass: 3060.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The sequence is chemically synthesized.
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.45 Å3/Da / Density % sol: 49.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Sodium Cacodylate, CaCl2, Spermine tetrahydrochloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1Sodium Cacodylate11
2CaCl211
3Spermine tetrahydrochloride11
4CaCl212
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.5 mMDNA1drop
225 mMsodium cacodylate1droppH7.
310 mM1dropCaCl2
42 mMspermine 4HCl1drop
520 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.15 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 22, 2001
RadiationMonochromator: Si 111 Chanel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.15 Å / Relative weight: 1
ReflectionResolution: 1.5→16.28 Å / Num. all: 7988 / Num. obs: 7988 / % possible obs: 87.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.043
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 0.325 / % possible all: 39.3
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 18200 / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
% possible obs: 39.3 % / Rmerge(I) obs: 0.435

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Processing

Software
NameVersionClassification
X-PLORCustom Script - Real Space translation/rotation/rigid body/rigid part searchmodel building
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORCUSTOM SCRIPT - REAL SPACE TRANSLATION/ROTATION/RIGID BODY/RIGID PART SEARCHphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→16.28 Å / TLS residual ADP flag: UNVERIFIED / σ(F): 0
Stereochemistry target values: G.PARKINSON, J. VOJTECHOVSKY, L. CLOWNEY, A.T. BRUNGER, H.M. BERMAN
RfactorNum. reflectionSelection details
Rfree0.264 852 Random
Rwork0.218 --
all0.223 7986 -
obs0.223 7986 -
Refinement stepCycle: LAST / Resolution: 1.5→16.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 3 95 502
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.012
X-RAY DIFFRACTIONr_angle_deg2.08
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
139.6562-65.3704-3.517365.7801-27.2352-30.5233-0.0841-0.903-0.50510.35130.15570.63481.1211-0.873-0.07160.2193-0.05090.02260.2019-0.01110.2009-23.5496-4.02131.58
219.0929-34.11746.40477.7498-3.74619.3486-0.39290.59980.22610.1842-0.5138-0.2891-0.47880.90310.90670.2135-0.0682-0.01040.2145-0.01630.2316-24.3518-2.243727.4043
373.64429.751-34.8349-31.1825-7.889612.61520.311-0.7572-0.50780.96-1.0112-0.45490.00840.54810.70020.2822-0.07080.00290.21120.0620.3076-20.2174-7.025931.7428
431.8458-16.4704-17.225760.776626.738815.3935-0.31050.0076-0.12670.0063-0.1597-0.6120.1935-0.27280.47010.178-0.07140.00540.22840.01830.229-19.7853-2.700129.4324
525.838831.5804-38.8855140.7212-1.7557-49.6423-1.0436-2.1748-2.3502-1.1715-0.0225-2.8706-0.20931.09381.06610.13610.00180.05310.18110.18670.5998-15.0534-8.631129.9965
619.3127-18.780327.775731.9537-18.558639.39740.0925-0.07490.260.11040.0654-0.07490.52520.362-0.1580.1474-0.07080.02130.21070.00770.239-15.7179-3.605128.5235
7-33.217635.687321.431697.48998.61159.6956-0.4664-0.8486-0.63430.06111.8361-0.94040.61180.1238-1.36970.11270.01850.29250.0525-0.02180.8587-11.8014-8.916124.7459
8-15.69486.3589-5.6967-1.18912.882617.72160.43530.22590.155-0.2832-0.5064-0.05620.42190.4380.07120.1603-0.04870.02510.2080.01050.2461-12.2614-3.857326.3341
910.1295-5.6539-56.9417-170.7949130.691839.3911-0.8956-0.3819-1.80194.3522-1.91742.0471.4498-0.16032.8130.2247-0.10520.05780.2145-0.10420.4111-9.8904-5.418420.2105
1086.2189-61.8312116.8995142.9202-175.8928172.10281.5859-0.12920.1968-0.3509-1.6707-1.11691.1662-0.06650.08480.1104-0.10230.00360.168-0.02120.2505-8.8316-3.272624.3849
1131.919724.233536.3879-3.2971-29.473537.58811.437-0.4494-0.3081-0.6766-1.5241-0.75931.5704-0.09250.08710.2338-0.00410.00370.2439-0.04640.1803-8.72960.193518.4519
12-18.6331-13.4605-29.399627.90513.805831.9223-0.13920.00190.0260.002-0.0358-0.29920.29060.12450.17490.1604-0.0896-0.00440.262-0.00310.2816-6.3843-0.594623.3958
1337.750814.606-13.72864.5721-32.8983127.27330.8822-0.57930.37410.2324-0.10170.2333-1.02020.6222-0.78040.16460.0241-0.03570.2349-0.05920.217-8.1584.92515.2207
14-32.740111.362311.335655.2677-12.455927.83290.07510.1836-0.4812-0.4189-0.3610.1893-0.1083-0.00290.28590.19040.0547-0.00070.2589-0.01790.2635-8.91811.559511.8048
1512.6731-22.819-0.302542.1537-45.611840.4101-1.22621.33170.11011.95410.6642-0.2658-1.14821.44360.5620.21410.0013-0.11550.1596-0.03770.2842-8.78239.050811.5989
165.526310.7363-24.53978.961933.2917-59.88560.34-0.5365-0.1510.1242-0.36540.130.26530.3460.02540.23530.011-0.03820.22940.02370.2299-11.90755.390712.2875
17-8.05112.0084-29.37452.3787-0.433-38.58420.1117-0.60180.0702-0.2074-0.7694-0.72210.35140.04970.65770.3115-0.0269-0.06310.1570.040.2908-12.117511.62767.4152
180.33594.89366.52593.5442-2.45477.9459-0.15930.0172-0.01790.0270.381-0.3305-0.18230.5346-0.22170.21870.0208-0.00810.22760.00940.2407-14.75327.86459.7921
1914.676610.3688-13.288357.6915-0.2695-6.0534-0.2504-1.0129-0.7037-1.1069-0.8841-1.5993-1.2908-1.22081.13450.27280.0084-0.04140.21180.08820.2113-15.840310.90272.8171
20-15.4863-8.6937-1.450861.2629-19.72231.9492-0.33640.1117-0.19550.0340.4591-0.2928-0.28230.1434-0.12270.16640.0389-0.00650.22760.00020.2463-17.88229.25217.4232
2127.027-16.3273-73.206-78.951826.996964.05520.16350.03070.0330.1312-0.02250.47821.15820.3953-0.14090.2593-0.0886-0.00990.2301-0.01650.21687.40012.181521.4797
22-26.6266-19.5159-3.596984.4258-21.67348.106-0.02330.23630.36770.4446-0.2828-0.2385-0.0441-0.11820.30610.1629-0.0792-0.00270.23720.00830.24976.03136.458322.4479
23-38.235428.726731.067825.7498-4.4404-8.0421-1.53830.6958-0.39090.19410.99440.10010.46760.49190.54390.22410.00430.03790.2499-0.03420.1966.3693-0.771324.8018
24-9.1722-22.2466-13.22721.3942-26.413109.1286-0.2350.29180.14520.5085-0.27680.5082-0.29470.19740.51190.1606-0.0568-0.00070.2508-0.02430.23773.07742.536423.1817
25-37.06456.114618.25912.334116.3855-18.4106-0.711-0.6349-0.1565-0.39060.6335-0.2131.29690.60830.07750.38330.01190.08610.18870.03830.22222.8543-2.542428.9653
266.86653.630315.88932.6342-7.4169-0.014-0.24630.2643-0.12610.06140.3957-0.19240.25850.766-0.14930.2269-0.03390.02290.23390.00850.22510.14250.696725.7545
27-10.166-2.57737.4818-24.22748.341647.9807-0.78350.0564-0.3690.14750.1313-0.01980.1707-0.6070.65230.2729-0.0380.03210.25310.05770.1649-1.2412-0.568833.1204
28-3.73927.791.067630.5541-26.982550.4288-0.3723-0.0949-0.3595-0.05420.47620.63860.6481-0.4029-0.10390.195-0.0334-0.00680.2160.00240.219-3.07860.194328.2931
29-16.00326.9011-13.93623.418223.867-96.1209-2.1464-1.5257-1.16150.86241.55330.4565-1.0846-0.72430.59310.30680.05570.01410.3860.05620.1338-6.16842.417433.3546
30-1.2355-39.6528-24.7245185.327212.4874-7.8355-0.2890.08470.02670.780.0739-0.84280.6503-0.34840.21510.18-0.0669-0.00440.26470.0120.229-6.3392-0.743829.3206
3122.5462-13.5536.698899.1579-0.68378.0557-1.0118-1.13860.19430.13341.51760.0263-1.2568-0.3291-0.50590.0939-0.07360.00320.3073-0.07150.1915-10.66935.516630.8363
325.0488-44.3188-17.944492.063617.895386.4322-0.04070.0734-0.1095-0.07670.0550.1749-0.0788-0.5013-0.01430.0834-0.0804-0.01130.2167-0.00940.2562-10.50291.091628.2487
3327.1955-26.83940.6267-39.9019-40.7519-26.2738-1.2519-0.88630.0119-0.4573-0.17822.2497-0.9802-0.09791.430.1979-0.0634-0.05480.1369-0.0060.3987-14.44336.137926.3795
34-17.681714.6612-32.706722.653630.3165107.12320.1292-0.50960.063-0.4661-0.2052-0.47210.0036-0.31360.0760.1066-0.0720.00470.2026-0.02430.2755-14.29131.348927.6848
3559.615571.8881-9.6549162.21341.5461-42.6892-1.48041.44550.75642.27281.39310.4064-0.94130.37480.08730.3146-0.1756-0.08330.28560.08020.1667-18.01373.755522.4572
368.2776-19.7388-2.811438.3785-3.8361.2367-0.2251-0.23120.4469-0.2035-0.3202-0.18670.22070.31540.54530.1741-0.0832-0.02430.21980.01990.2443-18.3581.179526.6899
37-41.0798-31.7196-17.019763.555723.701257.06080.29351.06080.2487-0.387-1.32180.57090.602-0.26071.02840.1749-0.10840.00530.33440.02440.1953-20.1023-0.58519.1224
384.4227-14.314111.42690.9409-10.587926.31610.28480.1522-0.0319-0.1219-0.5185-0.1114-0.46370.52550.23370.2111-0.08290.01730.2290.01550.257-21.0493-1.665524.0961
393.629-36.9332-21.006758.30329.851610.73680.5185-0.57150.4547-2.2513-0.80481.41230.78250.61650.28630.2532-0.0615-0.01660.233-0.01180.1486-21.5352-6.491317.9436
4010.6415-10.26064.483613.83114.819345.42190.24590.09880.2733-0.1429-0.36950.16570.2110.12960.12360.1695-0.08210.02590.21390.00250.2417-23.6308-4.618722.2279
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA11
2X-RAY DIFFRACTION2AA11
3X-RAY DIFFRACTION3AA22
4X-RAY DIFFRACTION4AA22
5X-RAY DIFFRACTION5AA33
6X-RAY DIFFRACTION6AA33
7X-RAY DIFFRACTION7AA44
8X-RAY DIFFRACTION8AA44
9X-RAY DIFFRACTION9AA55
10X-RAY DIFFRACTION10AA55
11X-RAY DIFFRACTION11AA66
12X-RAY DIFFRACTION12AA66
13X-RAY DIFFRACTION13AA77
14X-RAY DIFFRACTION14AA77
15X-RAY DIFFRACTION15AA88
16X-RAY DIFFRACTION16AA88
17X-RAY DIFFRACTION17AA99
18X-RAY DIFFRACTION18AA99
19X-RAY DIFFRACTION19AA1010
20X-RAY DIFFRACTION20AA1010
21X-RAY DIFFRACTION21BB111
22X-RAY DIFFRACTION22BB111
23X-RAY DIFFRACTION23BB122
24X-RAY DIFFRACTION24BB122
25X-RAY DIFFRACTION25BB133
26X-RAY DIFFRACTION26BB133
27X-RAY DIFFRACTION27BB144
28X-RAY DIFFRACTION28BB144
29X-RAY DIFFRACTION29BB155
30X-RAY DIFFRACTION30BB155
31X-RAY DIFFRACTION31BB166
32X-RAY DIFFRACTION32BB166
33X-RAY DIFFRACTION33BB177
34X-RAY DIFFRACTION34BB177
35X-RAY DIFFRACTION35BB188
36X-RAY DIFFRACTION36BB188
37X-RAY DIFFRACTION37BB199
38X-RAY DIFFRACTION38BB199
39X-RAY DIFFRACTION39BB2010
40X-RAY DIFFRACTION40BB2010
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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