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- PDB-1g6u: CRYSTAL STRUCTURE OF A DOMAIN SWAPPED DIMER -

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Basic information

Entry
Database: PDB / ID: 1g6u
TitleCRYSTAL STRUCTURE OF A DOMAIN SWAPPED DIMER
ComponentsDOMAIN SWAPPED DIMER
KeywordsDE NOVO PROTEIN / designed three helix bundle
Function / homologyHelix hairpin bin / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / trifluoroacetic acid
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.48 Å
AuthorsOgihara, N.L. / Ghirlanda, G. / Bryson, J.W. / Gingery, M. / DeGrado, W.F. / Eisenberg, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Design of three-dimensional domain-swapped dimers and fibrous oligomers.
Authors: Ogihara, N.L. / Ghirlanda, G. / Bryson, J.W. / Gingery, M. / DeGrado, W.F. / Eisenberg, D.
History
DepositionNov 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

Downloads & links

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Assembly

Deposited unit
A: DOMAIN SWAPPED DIMER
B: DOMAIN SWAPPED DIMER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4724
Polymers10,2622
Non-polymers2102
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-24 kcal/mol
Surface area6150 Å2
MethodPISA
2
A: DOMAIN SWAPPED DIMER
B: DOMAIN SWAPPED DIMER
hetero molecules

A: DOMAIN SWAPPED DIMER
B: DOMAIN SWAPPED DIMER
hetero molecules

A: DOMAIN SWAPPED DIMER
B: DOMAIN SWAPPED DIMER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,41612
Polymers30,7866
Non-polymers6306
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_564-z+1/2,-x+1,y-1/21
crystal symmetry operation10_655-y+1,z+1/2,-x+1/21
Buried area11190 Å2
ΔGint-102 kcal/mol
Surface area13450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.040, 64.040, 64.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11B-201-

SO4

21B-201-

SO4

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Components

#1: Protein/peptide DOMAIN SWAPPED DIMER


Mass: 5131.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The peptide was chemically synthesized.
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TFA / trifluoroacetic acid


Mass: 114.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2HF3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.13 Å3/Da / Density % sol: 42.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 100 mM MES, pH 6.5, 100 mM NaCl, 2.6 M ammonium sulfate, 1% dioxane, VAPOR DIFFUSION, temperature 298K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.6 Mammonium sulfate11
2100 mMMES11
3100 mM11NaCl
41 %dioxane11

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.975 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.48→30 Å / Num. all: 14554 / Num. obs: 14554 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.082
Reflection shellResolution: 1.48→1.57 Å / Rmerge(I) obs: 0.289 / Num. unique all: 2129 / % possible all: 88
Reflection
*PLUS
Num. measured all: 80427
Reflection shell
*PLUS
% possible obs: 94.1 %

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Processing

Software
NameVersionClassification
DMmodel building
X-PLOR3.82refinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: MIR / Resolution: 1.48→30 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1476 10.1 %RANDOM
Rwork0.198 ---
all0.202 14554 --
obs0.198 14554 97.9 %-
Displacement parametersBiso mean: 16.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.48→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms718 0 10 85 813
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_dihedral_angle_d16
X-RAY DIFFRACTIONx_improper_angle_d1.54
X-RAY DIFFRACTIONx_mcbond_it0.821.5
X-RAY DIFFRACTIONx_mcangle_it1.212
X-RAY DIFFRACTIONx_scbond_it3.662
X-RAY DIFFRACTIONx_scangle_it6.542.5
LS refinement shellResolution: 1.48→1.57 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.314 196 9.2 %
Rwork0.285 1933 -
obs-1934 88 %
Software
*PLUS
Name: X-PLOR(ONLINE) / Version: 3.82 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 16.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg16
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.54
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.314 / % reflection Rfree: 9.2 % / Rfactor Rwork: 0.285

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