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- PDB-1kyc: CRYSTAL STRUCTURE OF A DE NOVO DESIGNED TRIMERIC COILED-COIL PEPT... -

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Basic information

Entry
Database: PDB / ID: 1kyc
TitleCRYSTAL STRUCTURE OF A DE NOVO DESIGNED TRIMERIC COILED-COIL PEPTIDE STABLIZED BY IONIC INTERACTIONS
ComponentsSIN-GLU-GLU-LEU-ARG-ARG-ARG-ILE-GLU-GLU-LEU-GLU-ARG-ARG-ILE-ARG-NH2
KeywordsDE NOVO PROTEIN / COILED COIL / DE NOVO DESIGN / ALPHA-HELIX / TRIMER
Function / homologySUCCINIC ACID
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsBurkhard, P. / Ivaninskii, S. / Lustig, A.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Improving coiled-coil stability by optimizing ionic interactions.
Authors: Burkhard, P. / Ivaninskii, S. / Lustig, A.
#1: Journal: Protein Sci. / Year: 2000
Title: Design of a Minimal Protein Oligomerization Domain by a Structural Approach
Authors: Burkhard, P. / Meier, M. / Lustig, A.
History
DepositionFeb 4, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 24, 2020Group: Database references / Derived calculations / Source and taxonomy
Category: pdbx_entity_src_syn / struct_conn ...pdbx_entity_src_syn / struct_conn / struct_ref / struct_ref_seq
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific ..._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 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_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

Downloads & links

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Assembly

Deposited unit
A: SIN-GLU-GLU-LEU-ARG-ARG-ARG-ILE-GLU-GLU-LEU-GLU-ARG-ARG-ILE-ARG-NH2
A: SUCCINIC ACID
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,3684
Polymers2,0571
Non-polymers3103
Water41423
1
A: SIN-GLU-GLU-LEU-ARG-ARG-ARG-ILE-GLU-GLU-LEU-GLU-ARG-ARG-ILE-ARG-NH2
hetero molecules

A: SIN-GLU-GLU-LEU-ARG-ARG-ARG-ILE-GLU-GLU-LEU-GLU-ARG-ARG-ILE-ARG-NH2
hetero molecules

A: SIN-GLU-GLU-LEU-ARG-ARG-ARG-ILE-GLU-GLU-LEU-GLU-ARG-ARG-ILE-ARG-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,10312
Polymers6,1723
Non-polymers9319
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Unit cell
Length a, b, c (Å)33.386, 33.386, 65.691
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-101-

SO4

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Components

#1: Protein/peptide SIN-GLU-GLU-LEU-ARG-ARG-ARG-ILE-GLU-GLU-LEU-GLU-ARG-ARG-ILE-ARG-NH2


Mass: 2057.386 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This peptide was chemically synthesized. / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 1.71 Å3/Da / Density % sol: 28.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium sulfate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.600 mlsatammonium sulfate1reservoir
20.300 mlwater1reservoir
31 MHEPES1reservoirpH7.5
460.0 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 5, 2001
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. obs: 2574 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 10 % / Rsym value: 0.54 / Net I/σ(I): 20
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 7 / Rsym value: 0.131 / % possible all: 72.1
Reflection
*PLUS
Highest resolution: 1.45 Å / Lowest resolution: 30 Å / % possible obs: 96.9 % / Num. measured all: 47109 / Rmerge(I) obs: 0.54

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HQJ

1hqj


Resolution: 1.45→30 Å / Num. parameters: 1680 / Num. restraintsaints: 2133 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.217 -5 %
Rwork0.166 --
obs-2574 -
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 1384 / Occupancy sum non hydrogen: 1815
Refinement stepCycle: LAST / Resolution: 1.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms138 0 17 23 178
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d1.4
Refinement
*PLUS
Rfactor Rfree: 0.217 / Rfactor Rwork: 0.166
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg1.4

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