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- PDB-5xjz: Structure of DNA1-Ag complex -

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Basic information

Entry
Database: PDB / ID: 5xjz
TitleStructure of DNA1-Ag complex
ComponentsDNA (5'-D(*GP*CP*AP*CP*GP*CP*GP*C)-3')
KeywordsDNA / Ag / base pair
Function / homologySILVER ION / SPERMINE / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 0.98 Å
AuthorsLiu, H.H. / Gan, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31370728 China
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: A DNA Structure Containing AgI -Mediated G:G and C:C Base Pairs
Authors: Liu, H.H. / Shen, F.S. / Haruehanroengra, P. / Yao, Q.Q. / Cheng, Y.S. / Chen, Y.Q. / Yang, C. / Zhang, J. / Wu, B.X. / Luo, Q. / Cui, R.X. / Li, J.X. / Ma, J.B. / Sheng, J. / Gan, J.H.
History
DepositionMay 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_label_seq_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: DNA (5'-D(*GP*CP*AP*CP*GP*CP*GP*C)-3')
B: DNA (5'-D(*GP*CP*AP*CP*GP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,3516
Polymers4,8252
Non-polymers5264
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-12 kcal/mol
Surface area2550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.236, 42.546, 25.301
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-210-

HOH

21B-219-

HOH

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Components

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


Mass: 2412.594 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ag
#3: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.24 Å3/Da / Density % sol: 45.19 % / Description: Needle
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% v/v MPD, 40mM Sodium cacodylate pH 7.0, 12mM Spermine tetra-HCl, 80mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 0.98→30 Å / Num. obs: 24202 / % possible obs: 99.4 % / Redundancy: 6.4 % / Net I/σ(I): 31
Reflection shellResolution: 0.98→1.01 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1694 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 0.98→29.23 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.405 / SU ML: 0.01 / Cross valid method: THROUGHOUT / ESU R: 0.018 / ESU R Free: 0.017 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13065 1243 4.9 %RANDOM
Rwork0.12364 ---
obs0.12399 24202 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 10.719 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å2-0 Å20 Å2
2---0.44 Å20 Å2
3---0.33 Å2
Refinement stepCycle: 1 / Resolution: 0.98→29.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 320 17 83 420
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.011371
X-RAY DIFFRACTIONr_bond_other_d0.0050.02204
X-RAY DIFFRACTIONr_angle_refined_deg1.2761.195560
X-RAY DIFFRACTIONr_angle_other_deg1.5463478
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0660.248
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.02194
X-RAY DIFFRACTIONr_gen_planes_other0.0030.0292
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.5440.888371
X-RAY DIFFRACTIONr_scbond_other0.5430.891372
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.7341.32561
X-RAY DIFFRACTIONr_long_range_B_refined1.91210.049591
X-RAY DIFFRACTIONr_long_range_B_other1.3079.21547
X-RAY DIFFRACTIONr_rigid_bond_restr1.9933575
X-RAY DIFFRACTIONr_sphericity_free16.063513
X-RAY DIFFRACTIONr_sphericity_bonded5.5345614
LS refinement shellResolution: 0.98→1.006 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 98 -
Rwork0.35 1694 -
obs--96.76 %

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