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- PDB-1y47: Structural studies of designed alpha-helical hairpins -

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Basic information

Entry
Database: PDB / ID: 1y47
TitleStructural studies of designed alpha-helical hairpins
Componentsdueferri (DF2)
KeywordsDE NOVO PROTEIN / Protein design / helical hairpin / turns / diiron proteins
Function / homologyImmunoglobulin FC, subunit C / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha / :
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLahr, S.J. / Engel, D.E. / Stayrook, S.E. / Maglio, O. / North, B. / Geremia, S. / Lombardi, A. / DeGrado, W.F.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Analysis and design of turns in alpha-helical hairpins
Authors: Lahr, S.J. / Engel, D.E. / Stayrook, S.E. / Maglio, O. / North, B. / Geremia, S. / Lombardi, A. / DeGrado, W.F.
History
DepositionNov 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry / _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: dueferri (DF2)
B: dueferri (DF2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5385
Polymers11,2012
Non-polymers3373
Water543
1
A: dueferri (DF2)
hetero molecules

A: dueferri (DF2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4264
Polymers11,2012
Non-polymers2252
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area2370 Å2
ΔGint-39 kcal/mol
Surface area5640 Å2
MethodPISA, PQS
2
B: dueferri (DF2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8253
Polymers5,6001
Non-polymers2252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: dueferri (DF2)
hetero molecules

B: dueferri (DF2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6506
Polymers11,2012
Non-polymers4504
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)48.274, 39.017, 46.891
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-61-

HOH

21B-63-

HOH

Detailsthe biological assembly is a dimer generated by the two fold axis

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Components

#1: Protein/peptide dueferri (DF2)


Mass: 5600.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: designed peptide
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 1.7 Å3/Da / Density % sol: 31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 22% PEG MW 400, 0.1 M CdCl2, 0.1 M sodium acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 23, 2001 / Details: Osmic mirrors
RadiationMonochromator: Osmic Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→15 Å / Num. all: 2640 / Num. obs: 2625 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Biso Wilson estimate: 86.1 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08
Reflection shellResolution: 2.7→2.87 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.365 / Num. unique all: 379 / % possible all: 97.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EC5

1ec5


Resolution: 2.7→15 Å / Rfactor Rfree error: 0.02 / Data cutoff high absF: 492107.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 172 6.6 %RANDOM
Rwork0.234 ---
all0.236 2640 --
obs0.234 2625 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 83.7173 Å2 / ksol: 0.468996 e/Å3
Displacement parametersBiso mean: 62 Å2
Baniso -1Baniso -2Baniso -3
1--3.19 Å20 Å20 Å2
2---8.95 Å20 Å2
3---12.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms788 0 3 3 794
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d18.9
X-RAY DIFFRACTIONc_improper_angle_d0.65
X-RAY DIFFRACTIONc_mcbond_it2.331.5
X-RAY DIFFRACTIONc_mcangle_it3.992
X-RAY DIFFRACTIONc_scbond_it5.592
X-RAY DIFFRACTIONc_scangle_it7.882.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.062 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.337 30 7.3 %
Rwork0.274 379 -
obs--97.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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