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- PDB-3mbu: Structure of a bipyridine-modified PNA duplex -

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Basic information

Entry
Database: PDB / ID: 3mbu
TitleStructure of a bipyridine-modified PNA duplex
ComponentsBipyridine-PNA
KeywordsPeptide Nucleic acid / bipyridine / PNA
Function / homologyCARBONATE ION / S-1,2-PROPANEDIOL / R-1,2-PROPANEDIOL
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.05 Å
AuthorsYeh, J.I. / Pohl, E. / Truan, D. / He, W. / Sheldrick, G.M. / Du, S. / Achim, C.
CitationJournal: Chemistry / Year: 2010
Title: The crystal structure of non-modified and bipyridine-modified PNA duplexes.
Authors: Yeh, J.I. / Pohl, E. / Truan, D. / He, W. / Sheldrick, G.M. / Du, S. / Achim, C.
History
DepositionMar 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Structure summary / Category: audit_author / software / Item: _audit_author.name
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_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: Bipyridine-PNA
B: Bipyridine-PNA
C: Bipyridine-PNA
D: Bipyridine-PNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,22914
Polymers10,4834
Non-polymers74710
Water4,179232
1
A: Bipyridine-PNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,7593
Polymers2,6211
Non-polymers1382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bipyridine-PNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,7733
Polymers2,6211
Non-polymers1522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bipyridine-PNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,8494
Polymers2,6211
Non-polymers2283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bipyridine-PNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,8494
Polymers2,6211
Non-polymers2283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.200, 25.730, 53.050
Angle α, β, γ (deg.)90.00, 105.33, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-6045-

HOH

21C-6062-

HOH

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Components

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Protein/peptide , 1 types, 4 molecules ABCD

#1: Protein/peptide
Bipyridine-PNA


Mass: 2620.625 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Chemically synthesised

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Non-polymers , 6 types, 242 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PGR / R-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O2
#4: Chemical ChemComp-CO3 / CARBONATE ION / Carbonate


Mass: 60.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL / Propanediol


Mass: 76.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.72 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 5.5
Details: 40% propanediol 0.2 M NaCl 0.1 M citrate pH 5.5, VAPOR DIFFUSION, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X10SA10.8
SYNCHROTRONSLS X10SA20.8
Detector
IDDetector
1CCD
2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.05→50 Å / Num. all: 40632 / Num. obs: 34896 / Observed criterion σ(F): 4 / Observed criterion σ(I): 2

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Processing

Software
NameClassification
SHELXDphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.05→26.73 Å / Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): -3 / Details: conjugate gradient against intensities
RfactorNum. reflectionSelection details
Rfree0.169 2031 random
Rwork0.127 --
obs0.127 34896 -
all-40992 -
Refinement stepCycle: LAST / Resolution: 1.05→26.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms740 0 49 232 1021

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