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- PDB-1xj9: Crystal structure of a partly self-complementary peptide nucleic ... -

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Basic information

Entry
Database: PDB / ID: 1xj9
TitleCrystal structure of a partly self-complementary peptide nucleic acid (PNA) oligomer showing a duplex-triplex network
Componentspeptide nucleic acid, (H-P(*GPN*TPN*APN*GPN*APN*TPN*CPN*APN*CPN*TPN)-LYS-NH2)
KeywordsPEPTIDE NUCLEIC ACID / PNA / partly self-complementary / duplex-triplex complex / right-handed / left-handed
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / crystal 1: single wavelength protocol. crystal 2: MAD protocol with data collected on 5-bromo-uracil derivative crystal at 0.9177, 0.9185, 0.9110, 0.9218 A. the condition for crystal 2 was as follows. collection data: 05-NOV-2000, temperature(kelvin): 110, PH: 4.80, the details of the source of radiation: synchrotron, EMBL/DESY, HAMBURG beamline BW7A / Resolution: 2.6 Å
AuthorsPetersson, B. / Nielsen, B.B. / Rasmussen, H. / Larsen, I.K. / Gajhede, M. / Nielsen, P.E. / Kastrup, J.S.
Citation
Journal: J.Am.Chem.Soc. / Year: 2005
Title: Crystal Structure of a Partly Self-Complementary Peptide Nucleic Acid (PNA) Oligomer Showing a Duplex-Triplex Network
Authors: Petersson, B. / Nielsen, B.B. / Rasmussen, H. / Larsen, I.K. / Gajhede, M. / Nielsen, P.E. / Kastrup, J.S.
#1: Journal: Nat.Struct.Biol. / Year: 1997
Title: Crystal structure of a peptide nucleic acid (PNA) duplex at 1.7 A resolution
Authors: Rasmussen, H. / Kastrup, J.S. / Nielsen, J.N. / Nielsen, J.M. / Nielsen, P.E.
History
DepositionSep 23, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: peptide nucleic acid, (H-P(*GPN*TPN*APN*GPN*APN*TPN*CPN*APN*CPN*TPN)-LYS-NH2)
B: peptide nucleic acid, (H-P(*GPN*TPN*APN*GPN*APN*TPN*CPN*APN*CPN*TPN)-LYS-NH2)


Theoretical massNumber of molelcules
Total (without water)5,6082
Polymers5,6082
Non-polymers00
Water59433
1
A: peptide nucleic acid, (H-P(*GPN*TPN*APN*GPN*APN*TPN*CPN*APN*CPN*TPN)-LYS-NH2)

A: peptide nucleic acid, (H-P(*GPN*TPN*APN*GPN*APN*TPN*CPN*APN*CPN*TPN)-LYS-NH2)


Theoretical massNumber of molelcules
Total (without water)5,6082
Polymers5,6082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
2
B: peptide nucleic acid, (H-P(*GPN*TPN*APN*GPN*APN*TPN*CPN*APN*CPN*TPN)-LYS-NH2)

B: peptide nucleic acid, (H-P(*GPN*TPN*APN*GPN*APN*TPN*CPN*APN*CPN*TPN)-LYS-NH2)


Theoretical massNumber of molelcules
Total (without water)5,6082
Polymers5,6082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)55.600, 41.900, 30.100
Angle α, β, γ (deg.)90.00, 117.70, 90.00
Int Tables number5
Space group name H-MC121
DetailsTHIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS. A right-handed duplex (from chain A) is generated with the symmetry operation: -x+2, y, -z+1. / A left-handed duplex (from chain B) is generated with the symmetry operation: -x+1, y, -z

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Components

#1: DNA chain peptide nucleic acid, (H-P(*GPN*TPN*APN*GPN*APN*TPN*CPN*APN*CPN*TPN)-LYS-NH2) / / PNA


Mass: 2803.876 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.7755.59
2
Crystal grow
Temperature (K)Crystal-IDMethodDetails
2931vapor diffusion, hanging dropcrystal 1: magnesium chloride, PEG 8000, glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
2932vapor diffusion, sitting dropcrystal 2: isopropanol, calcium chloride, acetate, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1magnesium chloride11
2PEG 800011
3glycerol11
4H2O11
5PEG 800012
6H2O12
7isopropanol21
8calcium chloride21
9acetate21
10H2O21
11isopropanol22
12calcium chloride22
13acetate22
14H2O22

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 17, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 1839 / Num. obs: 1839 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 22.4
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 5.3 / Num. unique all: 172 / % possible all: 95.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: crystal 1: single wavelength protocol. crystal 2: MAD protocol with data collected on 5-bromo-uracil derivative crystal at 0.9177, 0.9185, 0.9110, 0.9218 A. the ...Method to determine structure: crystal 1: single wavelength protocol. crystal 2: MAD protocol with data collected on 5-bromo-uracil derivative crystal at 0.9177, 0.9185, 0.9110, 0.9218 A. the condition for crystal 2 was as follows. collection data: 05-NOV-2000, temperature(kelvin): 110, PH: 4.80, the details of the source of radiation: synchrotron, EMBL/DESY, HAMBURG beamline BW7A
Resolution: 2.6→27 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber / Details: Own parameter and topology files created
RfactorNum. reflection% reflectionSelection details
Rfree0.277 141 -random
Rwork0.255 ---
all-1839 --
obs-1517 78.2 %-
Displacement parametersBiso mean: 42.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.6→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms312 0 0 33 345
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.009
LS refinement shellResolution: 2.6→2.86 Å / Rfactor Rfree error: 0.092
RfactorNum. reflection% reflection
Rfree0.401 22 -
Rwork0.344 --
obs--70.9 %

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