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- PDB-5dsb: Crystal structure of Holliday junctions stabilized by 5-hydroxyme... -

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Basic information

Entry
Database: PDB / ID: 5dsb
TitleCrystal structure of Holliday junctions stabilized by 5-hydroxymethylcytosine in GCC junction core
Components5'-D(*CP*CP*GP*GP*CP*GP*5HCP*CP*GP*G)-3'
KeywordsDNA / Holliday junction / 5-hydroxymethylcytosine
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.4959 Å
AuthorsVander Zanden, C.M. / Rowe, R.K. / Broad, A.J. / Ho, P.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1F31GM1132580-01 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_symmetry / _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_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*5HCP*CP*GP*G)-3'
B: 5'-D(*CP*CP*GP*GP*CP*GP*5HCP*CP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1943
Polymers6,1542
Non-polymers401
Water1,65792
1
A: 5'-D(*CP*CP*GP*GP*CP*GP*5HCP*CP*GP*G)-3'
B: 5'-D(*CP*CP*GP*GP*CP*GP*5HCP*CP*GP*G)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)12,3886
Polymers12,3084
Non-polymers802
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2790 Å2
ΔGint-8 kcal/mol
Surface area6930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.073, 24.768, 38.061
Angle α, β, γ (deg.)90.000, 111.820, 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*5HCP*CP*GP*G)-3'


Mass: 3077.006 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.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.35 Å3/Da / Density % sol: 47.64 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.78 mM DNA, 0.8 mM Spermine, 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: Jan 28, 2015
RadiationMonochromator: Rigaku collimator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.4959→50 Å / Num. obs: 9346 / % possible obs: 99.3 % / Redundancy: 6.7 % / Biso Wilson estimate: 19.52 Å2 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.036 / Rrim(I) all: 0.123 / Χ2: 6.127 / Net I/av σ(I): 50.444 / Net I/σ(I): 14.9 / Num. measured all: 62380
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.4959-1.532.20.6394440.3180.4780.8023.79894.3
1.53-1.552.40.6074530.720.4480.7592.61896.8
1.55-1.582.50.364230.9010.2640.451.67497.5
1.58-1.622.70.2744820.9690.1970.341.58698
1.62-1.652.90.2624610.9690.180.321.57999.6
1.65-1.693.10.2214580.9740.1490.2681.62299.6
1.69-1.733.40.2544650.7440.1710.3093.30599.8
1.73-1.784.60.2644820.970.1370.2992.848100
1.78-1.835.20.3194570.9370.1560.3572.654100
1.83-1.895.70.3464730.9350.1580.3823.119100
1.89-1.966.10.4734490.9140.2030.5164.13100
1.96-2.046.50.254610.9510.1060.2722.974100
2.04-2.136.80.2224740.9710.0930.2413.834100
2.13-2.247.30.194890.9770.0770.2063.58100
2.24-2.389.10.4034660.9890.140.4285.421100
2.38-2.5610.10.1754600.9880.0570.1844.09100
2.56-2.8211.20.1484730.9930.0460.1565.693100
2.82-3.2312.30.1024910.9960.030.1067.207100
3.23-4.0713.60.0874730.9980.0250.09110.621100
4.07-5013.90.1095120.9880.0310.11313.347100

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHENIXphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1p4y

1p4y


Resolution: 1.4959→35.335 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 41.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2883 466 5.02 %random selection
Rwork0.2506 8822 --
obs0.2528 9288 98.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 40.62 Å2 / Biso mean: 25.3288 Å2 / Biso min: 12.81 Å2
Refinement stepCycle: final / Resolution: 1.4959→35.335 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 408 1 98 507
Biso mean--21.18 29.72 -
Num. residues----20
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011464
X-RAY DIFFRACTIONf_angle_d1.276716
X-RAY DIFFRACTIONf_chiral_restr0.04772
X-RAY DIFFRACTIONf_plane_restr0.0120
X-RAY DIFFRACTIONf_dihedral_angle_d44.647235
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4959-1.71240.40811500.33662817296795
1.7124-2.15740.33221630.32352952311599
2.1574-35.3450.25511530.218530533206100

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