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- PDB-1hqj: CRYSTAL STRUCTURE OF A DE NOVO DESIGNED TRIMERIC COILED-COIL PEPTIDE -

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Basic information

Entry
Database: PDB / ID: 1hqj
TitleCRYSTAL STRUCTURE OF A DE NOVO DESIGNED TRIMERIC COILED-COIL PEPTIDE
ComponentsSIN-ASP-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2
KeywordsDE NOVO PROTEIN / coiled coil / de novo design / alpha-helix / trimer
Function / homologyLEAD (II) ION / SUCCINIC ACID
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.2 Å
AuthorsBurkhard, P. / Meier, M. / Lustig, A.
CitationJournal: Protein Sci. / Year: 2000
Title: Design of a minimal protein oligomerization domain by a structural approach.
Authors: Burkhard, P. / Meier, M. / Lustig, A.
History
DepositionDec 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 3, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Oct 10, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / pdbx_entity_src_syn / struct_biol
Item: _entity.formula_weight / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.6Jul 24, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: entity / software / struct_conn
Item: _entity.formula_weight / _software.name / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SIN-ASP-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2
B: SIN-ASP-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2
C: SIN-ASP-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2
D: SIN-ASP-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2
E: SIN-ASP-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2
F: SIN-ASP-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2
G: SIN-ASP-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2
H: SIN-ASP-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2
I: SIN-ASP-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2
J: SIN-ASP-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2
K: SIN-ASP-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2
L: SIN-ASP-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,84137
Polymers23,17512
Non-polymers3,66625
Water2,648147
1
A: SIN-ASP-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2
B: SIN-ASP-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2
C: SIN-ASP-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5479
Polymers5,7943
Non-polymers7546
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-14 kcal/mol
Surface area3670 Å2
MethodPISA
2
D: SIN-ASP-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2
E: SIN-ASP-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2
F: SIN-ASP-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,86610
Polymers5,7943
Non-polymers1,0727
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-14 kcal/mol
Surface area3760 Å2
MethodPISA
3
G: SIN-ASP-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2
H: SIN-ASP-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2
I: SIN-ASP-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,86610
Polymers5,7943
Non-polymers1,0727
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-16 kcal/mol
Surface area3930 Å2
MethodPISA
4
J: SIN-ASP-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2
K: SIN-ASP-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2
L: SIN-ASP-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5628
Polymers5,7943
Non-polymers7695
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-15 kcal/mol
Surface area3760 Å2
MethodPISA
5
G: SIN-ASP-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2
H: SIN-ASP-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2
I: SIN-ASP-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2
J: SIN-ASP-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2
K: SIN-ASP-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2
L: SIN-ASP-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2
hetero molecules

A: SIN-ASP-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2
B: SIN-ASP-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2
C: SIN-ASP-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2
D: SIN-ASP-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2
E: SIN-ASP-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2
F: SIN-ASP-GLU-LEU-GLU-ALA-ARG-ILE-ARG-GLU-LEU-GLU-ALA-ARG-ILE-LYS-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,84137
Polymers23,17512
Non-polymers3,66625
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area15210 Å2
ΔGint-89 kcal/mol
Surface area11360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.334, 44.874, 81.043
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe peptide is a trimer at high ionic strength

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Components

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


Mass: 1931.222 Da / Num. of mol.: 12 / Source method: obtained synthetically / Details: Neosystem / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-PB / LEAD (II) ION / Lead


Mass: 207.200 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Pb
#3: Chemical
ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C4H6O4
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 1.74 Å3/Da / Density % sol: 29.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Ammonium Sulfate, Sodium Acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal
*PLUS
Density % sol: 25 %
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
21 Msodium acetate1reservoir
360 mg/mlprotein1drop
1ammonium sulfate1reservoir0.900ml saturated

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.951 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 5, 1999 / Details: WIGGLER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.951 Å / Relative weight: 1
ReflectionResolution: 1.2→30 Å / Num. all: 42926 / % possible obs: 81.2 % / Biso Wilson estimate: 12.8 Å2 / Rmerge(I) obs: 0.58
Reflection
*PLUS
Highest resolution: 1.2 Å / Lowest resolution: 30 Å / Num. obs: 78313 / % possible obs: 81.5 % / Num. measured all: 244675 / Rmerge(I) obs: 0.629

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Processing

Software
NameClassification
SHELXLrefinement
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 1.2→10 Å / Num. parameters: 1680 / Num. restraintsaints: 2133 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflection
Rfree0.223 -5 %
all0.17 4131 -
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 1384 / Occupancy sum non hydrogen: 1815
Refinement stepCycle: LAST / Resolution: 1.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1610 0 113 147 1870
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.004
X-RAY DIFFRACTIONs_angle_d0.9
Software
*PLUS
Name: SHELXL-96 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Num. reflection all: 78313 / Rfactor obs: 0.159 / Rfactor Rfree: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.5

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