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- PDB-1uno: Crystal structure of a d,l-alternating peptide -

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Basic information

Entry
Database: PDB / ID: 1uno
TitleCrystal structure of a d,l-alternating peptide
ComponentsH-(L-TYR-D-TYR)4-LYS-OH
KeywordsD-L PEPTIDE / D / L-ALTERNATING PEPTIDE / BETA-HELIX
Function / homologyH-(L-TYR-D-TYR)4-LYS-OH
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.4 Å
AuthorsAlexopoulos, E. / Kuesel, A. / Uson, I. / Diederichsen, U. / Sheldrick, G.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Solution and Structure of an Alternating D,L-Peptide
Authors: Alexopoulos, E. / Kuesel, A. / Sheldrick, G.M. / Diederichsen, U. / Uson, I.
History
DepositionSep 11, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2004Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2012Group: Other
Revision 1.2Feb 8, 2017Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Source and taxonomy / Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.5Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: H-(L-TYR-D-TYR)4-LYS-OH
B: H-(L-TYR-D-TYR)4-LYS-OH


Theoretical massNumber of molelcules
Total (without water)2,9052
Polymers2,9052
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)27.990, 27.990, 78.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein/peptide H-(L-TYR-D-TYR)4-LYS-OH


Type: Polypeptide / Class: Antibiotic / Mass: 1452.585 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) / References: H-(L-TYR-D-TYR)4-LYS-OH
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.66 Å3/Da / Density % sol: 40 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5 / Details: (NH4)2SO4,MPD,HEPES, PH 7.5,HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8015
DetectorDate: Jan 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8015 Å / Relative weight: 1
ReflectionResolution: 1.3→20 Å / Num. obs: 8289 / % possible obs: 91.2 % / Redundancy: 1.42 % / Rmerge(I) obs: 0.0339 / Net I/σ(I): 11.82
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.3083 / Mean I/σ(I) obs: 2.42 / % possible all: 93

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.4→20 Å / Num. parameters: 939 / Num. restraintsaints: 907 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2493 406 5 %IN THIN SHELLS
obs0.2216 -91.2 %-
all-8289 --
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 231
Refinement stepCycle: LAST / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms212 0 0 19 231
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.179
X-RAY DIFFRACTIONs_zero_chiral_vol0.072
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.1
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.02
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.046
X-RAY DIFFRACTIONs_approx_iso_adps

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