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- PDB-6m2p: Crystal structure of a NIR-emitting DNA-stabilized Ag16 nanoclust... -

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Entry
Database: PDB / ID: 6m2p
TitleCrystal structure of a NIR-emitting DNA-stabilized Ag16 nanocluster (A10-deletion mutant)
ComponentsDNA (5'-D(*CP*AP*CP*CP*TP*AP*GP*CP*G)-3')
KeywordsDNA / Nanocluster / Silver
Function / homologySILVER ION / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.13 Å
AuthorsKondo, J. / Cerretani, C. / Vosch, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
CitationJournal: Rsc Adv / Year: 2020
Title: Removal of the A10 adenosine in a DNA-stabilized Ag16 nanocluster.
Authors: Cerretani, C. / Kondo, J. / Vosch, T.
History
DepositionFeb 28, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 2.0Mar 22, 2023Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_type / chem_comp / database_2 / entity / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_contact_author / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] ..._atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _ndb_struct_na_base_pair_step.helical_rise / _ndb_struct_na_base_pair_step.helical_twist / _ndb_struct_na_base_pair_step.i_auth_asym_id_1 / _ndb_struct_na_base_pair_step.i_auth_seq_id_1 / _ndb_struct_na_base_pair_step.i_auth_seq_id_2 / _ndb_struct_na_base_pair_step.i_label_asym_id_1 / _ndb_struct_na_base_pair_step.i_label_comp_id_1 / _ndb_struct_na_base_pair_step.i_label_comp_id_2 / _ndb_struct_na_base_pair_step.i_label_seq_id_1 / _ndb_struct_na_base_pair_step.i_label_seq_id_2 / _ndb_struct_na_base_pair_step.inclination / _ndb_struct_na_base_pair_step.j_auth_asym_id_1 / _ndb_struct_na_base_pair_step.j_auth_seq_id_1 / _ndb_struct_na_base_pair_step.j_auth_seq_id_2 / _ndb_struct_na_base_pair_step.j_label_asym_id_1 / _ndb_struct_na_base_pair_step.j_label_seq_id_1 / _ndb_struct_na_base_pair_step.j_label_seq_id_2 / _ndb_struct_na_base_pair_step.rise / _ndb_struct_na_base_pair_step.roll / _ndb_struct_na_base_pair_step.shift / _ndb_struct_na_base_pair_step.slide / _ndb_struct_na_base_pair_step.step_name / _ndb_struct_na_base_pair_step.tilt / _ndb_struct_na_base_pair_step.tip / _ndb_struct_na_base_pair_step.twist / _ndb_struct_na_base_pair_step.x_displacement / _ndb_struct_na_base_pair_step.y_displacement / _pdbx_contact_author.id / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_rmsd_bond.auth_asym_id_1 / _pdbx_validate_rmsd_bond.auth_asym_id_2 / _pdbx_validate_rmsd_bond.auth_comp_id_1 / _pdbx_validate_rmsd_bond.auth_comp_id_2 / _pdbx_validate_rmsd_bond.auth_seq_id_1 / _pdbx_validate_rmsd_bond.auth_seq_id_2 / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _pdbx_validate_rmsd_bond.label_alt_id_1 / _pdbx_validate_rmsd_bond.label_alt_id_2 / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.d_res_high / _refine_hist.d_res_low / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_residues_total / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_restr.type / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_free_error / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.percent_reflns_obs / _software.classification / _software.name / _software.version / _struct_asym.entity_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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
Description: Ligand identity
Details: AG atoms with low occupancy are replaced with Cl ions according to our new experimental results by Mass Spectroscopy.
Provider: author / Type: Coordinate replacement
Revision 2.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)14,47742
Polymers10,8034
Non-polymers3,67438
Water1,856103
1
A: DNA (5'-D(*CP*AP*CP*CP*TP*AP*GP*CP*G)-3')
B: DNA (5'-D(*CP*AP*CP*CP*TP*AP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,23821
Polymers5,4022
Non-polymers1,83719
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (5'-D(*CP*AP*CP*CP*TP*AP*GP*CP*G)-3')
D: DNA (5'-D(*CP*AP*CP*CP*TP*AP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,23821
Polymers5,4022
Non-polymers1,83719
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.211, 33.713, 58.551
Angle α, β, γ (deg.)90.00, 98.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 2700.788 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: SF file contains Friedel pairs. / Source: (synth.) synthetic construct (others)
#2: Chemical...
ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: Ag / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.19 Å3/Da / Density % sol: 43.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: MOPS, MPD, Spermine, calcium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.125→29.142 Å / Num. obs: 67312 / % possible obs: 96.8 % / Redundancy: 3.406 % / Biso Wilson estimate: 4.16 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.059 / Χ2: 1.21 / Net I/σ(I): 16.89
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.13-1.153.2390.3593.2915726524948550.9040.4392.5
1.15-1.193.2260.2295.1114983492246440.960.27594.4
1.19-1.223.3310.1756.7315548492946670.9730.20994.7
1.22-1.263.4870.1448.3215673474044950.9810.1794.8
1.26-1.33.4490.10810.4715170458743990.9880.12895.9
1.3-1.353.3760.09411.4714405443742670.990.11296.2
1.35-1.43.2620.08811.9513408423741100.9910.10697
1.4-1.453.3470.0813.2413273408339660.9920.09597.1
1.45-1.523.5930.07115.4814067401239150.9940.08397.6
1.52-1.593.5270.06916.1113133379437240.9950.08198.2
1.59-1.683.4990.06416.9312176356134800.9960.07697.7
1.68-1.783.3270.05518.9311207341833690.9960.06598.6
1.78-1.93.2860.04223.1410372321131560.9980.0598.3
1.9-2.053.4030.03528.49907294629110.9980.04298.8
2.05-2.253.6180.02935.729829274327170.9990.03499.1
2.25-2.523.5770.02640.368711245224350.9990.0399.3
2.52-2.913.4640.02638.27509218721680.9990.03199.1
2.91-3.563.310.02834.196101185718430.9990.03499.2
3.56-5.033.620.02639.495119141814140.9990.03199.7
5.03-29.1423.7790.02246.3929367797770.9990.02699.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JR4

6jr4


Resolution: 1.13→29.14 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 6.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.096 1994 5.83 %
Rwork0.0853 --
obs0.0859 67302 96.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.13→29.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 716 38 103 857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011934
X-RAY DIFFRACTIONf_angle_d1.4471460
X-RAY DIFFRACTIONf_dihedral_angle_d28.815456
X-RAY DIFFRACTIONf_chiral_restr0.075180
X-RAY DIFFRACTIONf_plane_restr0.02246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.13-1.140.23581090.23792117X-RAY DIFFRACTION90
1.14-1.150.20181420.20512301X-RAY DIFFRACTION94
1.15-1.170.191430.16932138X-RAY DIFFRACTION94
1.17-1.180.13911360.13252203X-RAY DIFFRACTION94
1.18-1.20.12691310.122247X-RAY DIFFRACTION95
1.2-1.220.11411720.10262180X-RAY DIFFRACTION95
1.22-1.240.1251190.09362181X-RAY DIFFRACTION95
1.24-1.260.09251360.08842280X-RAY DIFFRACTION95
1.26-1.280.09071490.08662207X-RAY DIFFRACTION96
1.28-1.30.09011310.08762256X-RAY DIFFRACTION97
1.3-1.330.08871600.08892232X-RAY DIFFRACTION96
1.33-1.360.09571320.07492268X-RAY DIFFRACTION97
1.36-1.390.07341360.06912238X-RAY DIFFRACTION97
1.39-1.420.06491370.06512300X-RAY DIFFRACTION97
1.42-1.450.08511270.06482228X-RAY DIFFRACTION97
1.45-1.490.06991640.06242297X-RAY DIFFRACTION97
1.49-1.540.08831500.06512281X-RAY DIFFRACTION98
1.54-1.590.08461430.06452270X-RAY DIFFRACTION98
1.59-1.640.0711260.06872315X-RAY DIFFRACTION98
1.64-1.710.09581530.06932292X-RAY DIFFRACTION98
1.71-1.790.07851340.07212320X-RAY DIFFRACTION99
1.79-1.880.08361480.06972329X-RAY DIFFRACTION98
1.88-20.08991460.07262273X-RAY DIFFRACTION98
2-2.150.07121400.06892320X-RAY DIFFRACTION99
2.15-2.370.06881430.06092323X-RAY DIFFRACTION99
2.37-2.710.07061400.06542327X-RAY DIFFRACTION99
2.71-3.410.13451370.11422343X-RAY DIFFRACTION99
3.42-29.140.13461430.11742309X-RAY DIFFRACTION100

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