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- PDB-3c1p: Crystal Structure of an alternating D-Alanyl, L-Homoalanyl PNA -

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Basic information

Entry
Database: PDB / ID: 3c1p
TitleCrystal Structure of an alternating D-Alanyl, L-Homoalanyl PNA
ComponentsPeptide Nucleic Acid DLY-HGL-AGD-LHC-AGD-LHC-CUD-LYS
KeywordsPEPTIDE NUCLEIC ACID / Synthetic / PNA / alanyl / homoalanyl / DE NOVO PROTEIN
Function / homologyDLY-HGL-AGD-LHC-AGD-LHC-CUD-LYS / PEP_NUC
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1 Å
AuthorsCuesta-Seijo, J.A. / Sheldrick, G.M. / Zhang, J. / Diederichsen, U.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Continuous beta-turn fold of an alternating alanyl/homoalanyl peptide nucleic acid.
Authors: Cuesta-Seijo, J.A. / Zhang, J. / Diederichsen, U. / Sheldrick, G.M.
History
DepositionJan 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 25, 2012Group: Database references
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Jun 26, 2013Group: Database references
Revision 1.5Nov 26, 2014Group: Structure summary
Revision 2.0Mar 27, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy
Category: entity_poly / pdbx_entity_src_syn ...entity_poly / pdbx_entity_src_syn / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref / struct_ref_seq
Item: _entity_poly.type / _pdbx_entity_src_syn.ncbi_taxonomy_id ..._entity_poly.type / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_alt_id / _atom_site.label_atom_id / _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Peptide Nucleic Acid DLY-HGL-AGD-LHC-AGD-LHC-CUD-LYS
B: Peptide Nucleic Acid DLY-HGL-AGD-LHC-AGD-LHC-CUD-LYS
C: Peptide Nucleic Acid DLY-HGL-AGD-LHC-AGD-LHC-CUD-LYS
D: Peptide Nucleic Acid DLY-HGL-AGD-LHC-AGD-LHC-CUD-LYS


Theoretical massNumber of molelcules
Total (without water)6,0744
Polymers6,0744
Non-polymers00
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.308, 30.733, 33.550
Angle α, β, γ (deg.)90.00, 99.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Peptide nucleic acid
Peptide Nucleic Acid DLY-HGL-AGD-LHC-AGD-LHC-CUD-LYS


Type: Polypeptide / Class: Antibiotic / Mass: 1518.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Synthetic / Source: (synth.) synthetic construct (others) / References: DLY-HGL-AGD-LHC-AGD-LHC-CUD-LYS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.2 Å3/Da / Density % sol: 44.14 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1,6-hexanediol, MgCl2, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Components of the solutions
IDNameCrystal-IDSol-ID
11,6-hexanediol11
2MgCl211
3Tris-HCl11
4H2O11
51,6-hexanediol12
6MgCl212
7Tris-HCl12
8H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.7999 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 5, 2005 / Details: bendable mirror
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7999 Å / Relative weight: 1
ReflectionResolution: 1→40 Å / Num. all: 28613 / Num. obs: 28613 / % possible obs: 99.4 % / Redundancy: 12.99 % / Biso Wilson estimate: 12.7 Å2 / Rmerge(I) obs: 0.0639 / Rsym value: 0.0639 / Net I/σ(I): 18.13
Reflection shellResolution: 1→1.09 Å / Redundancy: 11.32 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 4.67 / Num. unique all: 6570 / Rsym value: 0.436 / % possible all: 98.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXDphasing
SHELXL-97refinement
XDSdata reduction
SADABSdata scaling
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1→40 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT
Stereochemistry target values: Parkinson for nucleobases, Engh & Huber for peptide part
Details: same distance restraints for link between peptide and nucleobases with no target values
RfactorNum. reflection% reflectionSelection details
Rfree0.2019 1425 5 %random
Rwork0.1503 ---
all0.1529 28537 --
obs0.1529 28537 99.1 %-
Displacement parametersBiso mean: 22.4 Å2
Refinement stepCycle: LAST / Resolution: 1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms397 0 0 140 537

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