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- PDB-3gnk: Calcium bound to the Holliday junction sequence d(TCGGCGCCGA)4 -

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Basic information

Entry
Database: PDB / ID: 3gnk
TitleCalcium bound to the Holliday junction sequence d(TCGGCGCCGA)4
Components5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3'
KeywordsDNA / Holliday junction Calcium ion Ca2+
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsNaseer, A. / Cardin, C.J.
CitationJournal: To be Published
Title: Calcium bound to the Holliday junction sequence d(TCGGCGCCGA)4
Authors: Naseer, A. / Cardin, C.J.
History
DepositionMar 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Sep 6, 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 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.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.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_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

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Assembly

Deposited unit
A: 5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3'
B: 5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3'
C: 5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3'
D: 5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3108
Polymers12,1844
Non-polymers1264
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-43 kcal/mol
Surface area6910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.9700, 24.1700, 73.8900
Angle α, β, γ (deg.)90.0000, 110.3700, 90.0000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-190-

HOH

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Components

#1: DNA chain
5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3'


Mass: 3045.992 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Holliday junctions
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.27 Å3/Da / Density % sol: 45.73 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: CaCl2, MPD, NaCacodylate , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K, temperature 290.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1CaCl211
2MPD11
3Na Cacodylate11
4CaCl212
5MPD12
6Na Cacodylate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418 Å
DetectorType: OXFORD SAPPHIRE CCD / Detector: CCD / Details: multilayer optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→16.347 Å / Num. all: 6643 / Num. obs: 6622 / % possible obs: 99.41 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Biso Wilson estimate: 17.122 Å2 / Limit h max: 29 / Limit h min: -31 / Limit k max: 11 / Limit k min: 0 / Limit l max: 35 / Limit l min: 0 / Rmerge(I) obs: 0.062 / Net I/σ(I): 11.44
Reflection scaleGroup code: 1
Reflection shellResolution: 2.1→2.155 Å / Redundancy: 3 % / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 2.35 / Num. unique all: 1773 / % possible all: 99.41

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT1.401data extraction
CrysalisProReddata collection
CrysalisProReddata reduction
MOLREPphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1L4J

1l4j


Resolution: 2.1→16.347 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.872 / SU B: 5.862 / SU ML: 0.158 / SU R Cruickshank DPI: 0.299 / Cross valid method: THROUGHOUT / ESU R Free: 0.26
RfactorNum. reflection% reflectionSelection details
Rfree0.306 311 4.7 %RANDOM
Rwork0.214 ---
all0.218 6622 --
obs0.218 6622 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.122 Å2
Baniso -1Baniso -2Baniso -3
1--1.24 Å20 Å20.06 Å2
2--1.3 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→16.347 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 808 4 183 995
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONr_bond_refined_d0.0059040.021
X-RAY DIFFRACTIONr_angle_refined_deg1.28513883
X-RAY DIFFRACTIONr_chiral_restr0.0531560.2
X-RAY DIFFRACTIONr_gen_planes_refined0.0054160.02
X-RAY DIFFRACTIONr_nbd_refined0.1622690.2
X-RAY DIFFRACTIONr_nbtor_refined0.2935150.2
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1191700.2
X-RAY DIFFRACTIONPOTENTIAL METAL-ION REFINED ATOMS (A)0.16370.2
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.098350.2
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.071130.2
X-RAY DIFFRACTIONr_scbond_it0.71611033
X-RAY DIFFRACTIONr_scangle_it1.07913884.5
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 28 -
Rwork0.256 453 -
obs-6622 98.97 %

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