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- PDB-1zez: ACC Holliday Junction -

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Basic information

Entry
Database: PDB / ID: 1zez
TitleACC Holliday Junction
Components5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3'
KeywordsDNA / Crystallographic Screen / DNA Structure / Holliday Junction / Molecular Structure
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHays, F.A. / Teegarden, A.T. / Jones, Z.J.R. / Harms, M. / Raup, D. / Watson, J. / Cavaliere, E. / Ho, P.S.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: How sequence defines structure: a crystallographic map of DNA structure and conformation.
Authors: Hays, F.A. / Teegarden, A. / Jones, Z.J. / Harms, M. / Raup, D. / Watson, J. / Cavaliere, E. / Ho, P.S.
History
DepositionApr 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Feb 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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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


Theoretical massNumber of molelcules
Total (without water)6,1323
Polymers6,0922
Non-polymers401
Water1,27971
1
A: 5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3'
B: 5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)12,2646
Polymers12,1844
Non-polymers802
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)66.02, 24.12, 36.88
Angle α, β, γ (deg.)90.0, 110.08, 90.0
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-37-

HOH

21B-62-

HOH

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Components

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


Mass: 3045.992 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: DNA WAS SYNTHESIZED ON AN APPLIED BIOSYSTEMS DNA SYNTHESIZER USING PHOSPHORAMIDITE CHEMISTRY, WITH THE TRITYL-PROTECTING GROUP LEFT INTACT AT THE 5'- TERMINAL NUCLEOTIDE THEN DEPROTECTED BY ...Details: DNA WAS SYNTHESIZED ON AN APPLIED BIOSYSTEMS DNA SYNTHESIZER USING PHOSPHORAMIDITE CHEMISTRY, WITH THE TRITYL-PROTECTING GROUP LEFT INTACT AT THE 5'- TERMINAL NUCLEOTIDE THEN DEPROTECTED BY TREATMENT WITH 3% ACETIC ACID FOR FIFTEEN MINUTES, NEUTRALIZED WITH AMMONIUM HYDROXIDE, AND DESALTED ON A SIGMA G-25 SEPHADEX COLUMN.
#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.: 71 / 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: 2.26 Å3/Da / Density % sol: 45.66 %
Crystal growTemperature: 298 K / pH: 7
Details: Na Cacodylate, CaCl2, Spermine, MPD in resevoir, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 7.00
Components of the solutions
IDNameCrystal-IDSol-ID
1Na Cacodylate11
2CaCl211
3Spermine11
4MPD11
5H2O11
6Na Cacodylate12
7CaCl212
8MPD12
9H2O12

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.542
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 13, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. obs: 3789 / % possible obs: 91.8 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 7.9 Å2 / Rmerge(I) obs: 0.074
Reflection shellResolution: 1.95→2.02 Å / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.65 / Rsym value: 0.57 / % possible all: 67.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ndb entry UD0008

Resolution: 2→17.98 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 39820.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: STRUCTURE IS NOT REFINED TO ITS LOWEST R VALUES. REFER TO CITED PUBLICATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.279 346 10 %RANDOM
Rwork0.229 ---
obs0.229 3443 90 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 74.665 Å2 / ksol: 0.344309 e/Å3
Displacement parametersBiso mean: 13.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å2-0.87 Å2
2--4.67 Å20 Å2
3----4.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2→17.98 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms0 0 0 0 0
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.66
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.017
X-RAY DIFFRACTIONc_mcangle_it0.0230
X-RAY DIFFRACTIONc_scbond_it0.0880
X-RAY DIFFRACTIONc_scangle_it0.1480
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.047 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.312 44 9.6 %
Rwork0.289 413 -
obs--74.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:DNA-RNA_REP.PARAMCNS_TOPPAR:DNA-RNA.TOP
X-RAY DIFFRACTION2CNS_TOPPAR:WATER_REP.PARAMCNS_TOPPAR:DNA-RNA.LINK
X-RAY DIFFRACTION3CNS_TOPPAR:ION.PARAMCNS_TOPPAR:WATER.TOP
X-RAY DIFFRACTION4CNS_TOPPAR:ION.TOP

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