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- PDB-5dsa: Crystal structure of Holliday junctions stabilized by 5-methylcyt... -

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Basic information

Entry
Database: PDB / ID: 5dsa
TitleCrystal structure of Holliday junctions stabilized by 5-methylcytosine in GCC junction core
Components5'-D(*CP*CP*GP*GP*CP*GP*5CMP*CP*GP*G)-3'
KeywordsDNA / Holliday junction / 5-methylcytosine
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6896 Å
AuthorsVander Zanden, C.M. / Ho, P.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1F31GM113580-01 United States
CitationJournal: Biochemistry / Year: 2016
Title: Effect of Hydroxymethylcytosine on the Structure and Stability of Holliday Junctions.
Authors: Vander Zanden, C.M. / Rowe, R.K. / Broad, A.J. / Robertson, A.B. / Ho, P.S.
History
DepositionSep 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Oct 19, 2016Group: Database references
Revision 1.3Feb 1, 2017Group: Database references
Revision 1.4Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.6Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.7Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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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*CP*GP*5CMP*CP*GP*G)-3'
B: 5'-D(*CP*CP*GP*GP*CP*GP*5CMP*CP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2024
Polymers6,1222
Non-polymers802
Water1,56787
1
A: 5'-D(*CP*CP*GP*GP*CP*GP*5CMP*CP*GP*G)-3'
B: 5'-D(*CP*CP*GP*GP*CP*GP*5CMP*CP*GP*G)-3'
hetero molecules

A: 5'-D(*CP*CP*GP*GP*CP*GP*5CMP*CP*GP*G)-3'
B: 5'-D(*CP*CP*GP*GP*CP*GP*5CMP*CP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4048
Polymers12,2444
Non-polymers1604
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5530 Å2
ΔGint-22 kcal/mol
Surface area6220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.968, 24.542, 37.992
Angle α, β, γ (deg.)90.000, 111.980, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: DNA chain 5'-D(*CP*CP*GP*GP*CP*GP*5CMP*CP*GP*G)-3'


Mass: 3061.008 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.33 Å3/Da / Density % sol: 47.19 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.78 mM DNA, 1.0 mM Spermine, 3.5 mM CaCl2, 25 mM sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Oct 8, 2014
RadiationMonochromator: Rigaku collimator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. obs: 6159 / % possible obs: 91.8 % / Redundancy: 6 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.023 / Rrim(I) all: 0.072 / Χ2: 3.208 / Net I/av σ(I): 51 / Net I/σ(I): 20.7 / Num. measured all: 36747
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.68-1.712.10.245720.9520.1730.3021.34223.2
1.71-1.742.30.2052730.9750.1450.2532.37879.6
1.74-1.772.60.1812850.9880.1210.2192.05185.3
1.77-1.8130.2272710.9550.1430.271.83186.9
1.81-1.853.10.253010.9560.1590.2981.74188.8
1.85-1.893.20.2873150.9480.1780.341.94590.8
1.89-1.943.30.1942950.9530.1160.2273.22591.9
1.94-1.993.40.23120.9670.1210.2352.02594.3
1.99-2.053.50.1433240.9760.0850.1671.83495
2.05-2.123.60.1213120.9840.0720.1421.6296.3
2.12-2.193.80.1113300.9880.0620.1281.79397.9
2.19-2.284.20.1583330.9820.0770.1775.0199.7
2.28-2.386.40.1653350.9930.0680.1793.16100
2.38-2.517.70.153420.9940.0550.163.018100
2.51-2.678.50.123290.9950.0420.1272.836100
2.67-2.879.20.0983390.9980.0330.1032.81100
2.87-3.1610.20.0653410.9990.020.0693.071100
3.16-3.6211.20.0583370.9990.0170.063.785100
3.62-4.5611.80.0583480.9980.0170.0614.085100
4.56-509.50.063650.9990.020.0634.45699.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P4Y

1p4y


Resolution: 1.6896→30.587 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2775 300 4.91 %random selection
Rwork0.248 5816 --
obs0.2495 6116 93.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 47.84 Å2 / Biso mean: 27.315 Å2 / Biso min: 16.38 Å2
Refinement stepCycle: final / Resolution: 1.6896→30.587 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 406 2 87 495
Biso mean--22.3 31.56 -
Num. residues----20
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009454
X-RAY DIFFRACTIONf_angle_d1.187698
X-RAY DIFFRACTIONf_chiral_restr0.04976
X-RAY DIFFRACTIONf_plane_restr0.0120
X-RAY DIFFRACTIONf_dihedral_angle_d36.914180
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6896-2.12870.36851330.30672700283388
2.1287-30.59150.25751670.23293116328399

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